Starting phenix.real_space_refine on Tue Aug 26 10:43:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8wiq_37566/08_2025/8wiq_37566.cif Found real_map, /net/cci-nas-00/data/ceres_data/8wiq_37566/08_2025/8wiq_37566.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.19 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8wiq_37566/08_2025/8wiq_37566.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8wiq_37566/08_2025/8wiq_37566.map" model { file = "/net/cci-nas-00/data/ceres_data/8wiq_37566/08_2025/8wiq_37566.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8wiq_37566/08_2025/8wiq_37566.cif" } resolution = 2.19 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= 0.048 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 168 5.16 5 C 23328 2.51 5 N 6432 2.21 5 O 7152 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 240 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 37080 Number of models: 1 Model: "" Number of chains: 24 Chain: "A" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "B" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "C" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "D" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "E" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "F" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "G" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "H" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "I" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "J" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "K" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "L" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "M" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "N" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "O" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "P" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "Q" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "R" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "S" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "T" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "U" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "V" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "W" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Chain: "X" Number of atoms: 1545 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1545 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 3, 'TRANS': 183} Chain breaks: 1 Time building chain proxies: 6.90, per 1000 atoms: 0.19 Number of scatterers: 37080 At special positions: 0 Unit cell: (137.31, 137.31, 137.31, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 168 16.00 O 7152 8.00 N 6432 7.00 C 23328 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.60 Conformation dependent library (CDL) restraints added in 1.3 seconds Enol-peptide restraints added in 953.7 nanoseconds 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 8688 Finding SS restraints... Secondary structure from input PDB file: 192 helices and 0 sheets defined 79.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid -22 through -15 Processing helix chain 'A' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU A -8 " --> pdb=" O SER A -11 " (cutoff:3.500A) Processing helix chain 'A' and resid 14 through 42 Processing helix chain 'A' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY A 78 " --> pdb=" O GLN A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 138 Processing helix chain 'A' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY A 160 " --> pdb=" O LEU A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU A 168 " --> pdb=" O SER A 164 " (cutoff:3.500A) Processing helix chain 'B' and resid -21 through -15 Processing helix chain 'B' and resid -13 through -8 removed outlier: 4.250A pdb=" N LEU B -8 " --> pdb=" O SER B -11 " (cutoff:3.500A) Processing helix chain 'B' and resid 14 through 42 Processing helix chain 'B' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY B 78 " --> pdb=" O GLN B 74 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS B 125 " --> pdb=" O LEU B 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 127 through 138 Processing helix chain 'B' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY B 160 " --> pdb=" O LEU B 156 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU B 168 " --> pdb=" O SER B 164 " (cutoff:3.500A) Processing helix chain 'C' and resid -21 through -15 Processing helix chain 'C' and resid -13 through -8 removed outlier: 4.252A pdb=" N LEU C -8 " --> pdb=" O SER C -11 " (cutoff:3.500A) Processing helix chain 'C' and resid 14 through 42 Processing helix chain 'C' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY C 78 " --> pdb=" O GLN C 74 " (cutoff:3.500A) Processing helix chain 'C' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS C 125 " --> pdb=" O LEU C 121 " (cutoff:3.500A) Processing helix chain 'C' and resid 127 through 138 Processing helix chain 'C' and resid 138 through 160 removed outlier: 3.671A pdb=" N GLY C 160 " --> pdb=" O LEU C 156 " (cutoff:3.500A) Processing helix chain 'C' and resid 164 through 175 removed outlier: 3.763A pdb=" N GLU C 168 " --> pdb=" O SER C 164 " (cutoff:3.500A) Processing helix chain 'D' and resid -21 through -15 Processing helix chain 'D' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU D -8 " --> pdb=" O SER D -11 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 42 Processing helix chain 'D' and resid 49 through 78 removed outlier: 3.500A pdb=" N GLY D 78 " --> pdb=" O GLN D 74 " (cutoff:3.500A) Processing helix chain 'D' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS D 125 " --> pdb=" O LEU D 121 " (cutoff:3.500A) Processing helix chain 'D' and resid 127 through 138 Processing helix chain 'D' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY D 160 " --> pdb=" O LEU D 156 " (cutoff:3.500A) Processing helix chain 'D' and resid 164 through 175 removed outlier: 3.763A pdb=" N GLU D 168 " --> pdb=" O SER D 164 " (cutoff:3.500A) Processing helix chain 'E' and resid -21 through -15 Processing helix chain 'E' and resid -13 through -8 removed outlier: 4.252A pdb=" N LEU E -8 " --> pdb=" O SER E -11 " (cutoff:3.500A) Processing helix chain 'E' and resid 14 through 42 Processing helix chain 'E' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY E 78 " --> pdb=" O GLN E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS E 125 " --> pdb=" O LEU E 121 " (cutoff:3.500A) Processing helix chain 'E' and resid 127 through 138 Processing helix chain 'E' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY E 160 " --> pdb=" O LEU E 156 " (cutoff:3.500A) Processing helix chain 'E' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU E 168 " --> pdb=" O SER E 164 " (cutoff:3.500A) Processing helix chain 'F' and resid -21 through -15 Processing helix chain 'F' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU F -8 " --> pdb=" O SER F -11 " (cutoff:3.500A) Processing helix chain 'F' and resid 14 through 42 Processing helix chain 'F' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY F 78 " --> pdb=" O GLN F 74 " (cutoff:3.500A) Processing helix chain 'F' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS F 125 " --> pdb=" O LEU F 121 " (cutoff:3.500A) Processing helix chain 'F' and resid 127 through 138 Processing helix chain 'F' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY F 160 " --> pdb=" O LEU F 156 " (cutoff:3.500A) Processing helix chain 'F' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU F 168 " --> pdb=" O SER F 164 " (cutoff:3.500A) Processing helix chain 'G' and resid -21 through -15 Processing helix chain 'G' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU G -8 " --> pdb=" O SER G -11 " (cutoff:3.500A) Processing helix chain 'G' and resid 14 through 42 Processing helix chain 'G' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY G 78 " --> pdb=" O GLN G 74 " (cutoff:3.500A) Processing helix chain 'G' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS G 125 " --> pdb=" O LEU G 121 " (cutoff:3.500A) Processing helix chain 'G' and resid 127 through 138 Processing helix chain 'G' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY G 160 " --> pdb=" O LEU G 156 " (cutoff:3.500A) Processing helix chain 'G' and resid 164 through 175 removed outlier: 3.763A pdb=" N GLU G 168 " --> pdb=" O SER G 164 " (cutoff:3.500A) Processing helix chain 'H' and resid -21 through -15 Processing helix chain 'H' and resid -13 through -8 removed outlier: 4.252A pdb=" N LEU H -8 " --> pdb=" O SER H -11 " (cutoff:3.500A) Processing helix chain 'H' and resid 14 through 42 Processing helix chain 'H' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY H 78 " --> pdb=" O GLN H 74 " (cutoff:3.500A) Processing helix chain 'H' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS H 125 " --> pdb=" O LEU H 121 " (cutoff:3.500A) Processing helix chain 'H' and resid 127 through 138 Processing helix chain 'H' and resid 138 through 160 removed outlier: 3.671A pdb=" N GLY H 160 " --> pdb=" O LEU H 156 " (cutoff:3.500A) Processing helix chain 'H' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU H 168 " --> pdb=" O SER H 164 " (cutoff:3.500A) Processing helix chain 'I' and resid -21 through -15 Processing helix chain 'I' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU I -8 " --> pdb=" O SER I -11 " (cutoff:3.500A) Processing helix chain 'I' and resid 14 through 42 Processing helix chain 'I' and resid 49 through 78 removed outlier: 3.500A pdb=" N GLY I 78 " --> pdb=" O GLN I 74 " (cutoff:3.500A) Processing helix chain 'I' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS I 125 " --> pdb=" O LEU I 121 " (cutoff:3.500A) Processing helix chain 'I' and resid 127 through 138 Processing helix chain 'I' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY I 160 " --> pdb=" O LEU I 156 " (cutoff:3.500A) Processing helix chain 'I' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU I 168 " --> pdb=" O SER I 164 " (cutoff:3.500A) Processing helix chain 'J' and resid -21 through -15 Processing helix chain 'J' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU J -8 " --> pdb=" O SER J -11 " (cutoff:3.500A) Processing helix chain 'J' and resid 14 through 42 Processing helix chain 'J' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY J 78 " --> pdb=" O GLN J 74 " (cutoff:3.500A) Processing helix chain 'J' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS J 125 " --> pdb=" O LEU J 121 " (cutoff:3.500A) Processing helix chain 'J' and resid 127 through 138 Processing helix chain 'J' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY J 160 " --> pdb=" O LEU J 156 " (cutoff:3.500A) Processing helix chain 'J' and resid 164 through 175 removed outlier: 3.763A pdb=" N GLU J 168 " --> pdb=" O SER J 164 " (cutoff:3.500A) Processing helix chain 'K' and resid -21 through -15 Processing helix chain 'K' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU K -8 " --> pdb=" O SER K -11 " (cutoff:3.500A) Processing helix chain 'K' and resid 14 through 42 Processing helix chain 'K' and resid 49 through 78 removed outlier: 3.500A pdb=" N GLY K 78 " --> pdb=" O GLN K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS K 125 " --> pdb=" O LEU K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 127 through 138 Processing helix chain 'K' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY K 160 " --> pdb=" O LEU K 156 " (cutoff:3.500A) Processing helix chain 'K' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU K 168 " --> pdb=" O SER K 164 " (cutoff:3.500A) Processing helix chain 'L' and resid -21 through -15 Processing helix chain 'L' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU L -8 " --> pdb=" O SER L -11 " (cutoff:3.500A) Processing helix chain 'L' and resid 14 through 42 Processing helix chain 'L' and resid 49 through 78 removed outlier: 3.500A pdb=" N GLY L 78 " --> pdb=" O GLN L 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS L 125 " --> pdb=" O LEU L 121 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 138 Processing helix chain 'L' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY L 160 " --> pdb=" O LEU L 156 " (cutoff:3.500A) Processing helix chain 'L' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU L 168 " --> pdb=" O SER L 164 " (cutoff:3.500A) Processing helix chain 'M' and resid -21 through -15 Processing helix chain 'M' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU M -8 " --> pdb=" O SER M -11 " (cutoff:3.500A) Processing helix chain 'M' and resid 14 through 42 Processing helix chain 'M' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY M 78 " --> pdb=" O GLN M 74 " (cutoff:3.500A) Processing helix chain 'M' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS M 125 " --> pdb=" O LEU M 121 " (cutoff:3.500A) Processing helix chain 'M' and resid 127 through 138 Processing helix chain 'M' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY M 160 " --> pdb=" O LEU M 156 " (cutoff:3.500A) Processing helix chain 'M' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU M 168 " --> pdb=" O SER M 164 " (cutoff:3.500A) Processing helix chain 'N' and resid -21 through -15 Processing helix chain 'N' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU N -8 " --> pdb=" O SER N -11 " (cutoff:3.500A) Processing helix chain 'N' and resid 14 through 42 Processing helix chain 'N' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY N 78 " --> pdb=" O GLN N 74 " (cutoff:3.500A) Processing helix chain 'N' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS N 125 " --> pdb=" O LEU N 121 " (cutoff:3.500A) Processing helix chain 'N' and resid 127 through 138 Processing helix chain 'N' and resid 138 through 160 removed outlier: 3.671A pdb=" N GLY N 160 " --> pdb=" O LEU N 156 " (cutoff:3.500A) Processing helix chain 'N' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU N 168 " --> pdb=" O SER N 164 " (cutoff:3.500A) Processing helix chain 'O' and resid -21 through -15 Processing helix chain 'O' and resid -13 through -8 removed outlier: 4.252A pdb=" N LEU O -8 " --> pdb=" O SER O -11 " (cutoff:3.500A) Processing helix chain 'O' and resid 14 through 42 Processing helix chain 'O' and resid 49 through 78 removed outlier: 3.502A pdb=" N GLY O 78 " --> pdb=" O GLN O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS O 125 " --> pdb=" O LEU O 121 " (cutoff:3.500A) Processing helix chain 'O' and resid 127 through 138 Processing helix chain 'O' and resid 138 through 160 removed outlier: 3.669A pdb=" N GLY O 160 " --> pdb=" O LEU O 156 " (cutoff:3.500A) Processing helix chain 'O' and resid 164 through 175 removed outlier: 3.705A pdb=" N GLU O 168 " --> pdb=" O SER O 164 " (cutoff:3.500A) Processing helix chain 'P' and resid -21 through -15 Processing helix chain 'P' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU P -8 " --> pdb=" O SER P -11 " (cutoff:3.500A) Processing helix chain 'P' and resid 14 through 42 Processing helix chain 'P' and resid 49 through 78 removed outlier: 3.500A pdb=" N GLY P 78 " --> pdb=" O GLN P 74 " (cutoff:3.500A) Processing helix chain 'P' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS P 125 " --> pdb=" O LEU P 121 " (cutoff:3.500A) Processing helix chain 'P' and resid 127 through 138 Processing helix chain 'P' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY P 160 " --> pdb=" O LEU P 156 " (cutoff:3.500A) Processing helix chain 'P' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU P 168 " --> pdb=" O SER P 164 " (cutoff:3.500A) Processing helix chain 'Q' and resid -21 through -15 Processing helix chain 'Q' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU Q -8 " --> pdb=" O SER Q -11 " (cutoff:3.500A) Processing helix chain 'Q' and resid 14 through 42 Processing helix chain 'Q' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY Q 78 " --> pdb=" O GLN Q 74 " (cutoff:3.500A) Processing helix chain 'Q' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS Q 125 " --> pdb=" O LEU Q 121 " (cutoff:3.500A) Processing helix chain 'Q' and resid 127 through 138 Processing helix chain 'Q' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY Q 160 " --> pdb=" O LEU Q 156 " (cutoff:3.500A) Processing helix chain 'Q' and resid 164 through 175 removed outlier: 3.694A pdb=" N GLU Q 168 " --> pdb=" O SER Q 164 " (cutoff:3.500A) Processing helix chain 'R' and resid -21 through -15 Processing helix chain 'R' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU R -8 " --> pdb=" O SER R -11 " (cutoff:3.500A) Processing helix chain 'R' and resid 14 through 42 Processing helix chain 'R' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY R 78 " --> pdb=" O GLN R 74 " (cutoff:3.500A) Processing helix chain 'R' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS R 125 " --> pdb=" O LEU R 121 " (cutoff:3.500A) Processing helix chain 'R' and resid 127 through 138 Processing helix chain 'R' and resid 138 through 160 removed outlier: 3.671A pdb=" N GLY R 160 " --> pdb=" O LEU R 156 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 175 removed outlier: 3.763A pdb=" N GLU R 168 " --> pdb=" O SER R 164 " (cutoff:3.500A) Processing helix chain 'S' and resid -21 through -15 Processing helix chain 'S' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU S -8 " --> pdb=" O SER S -11 " (cutoff:3.500A) Processing helix chain 'S' and resid 14 through 42 Processing helix chain 'S' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY S 78 " --> pdb=" O GLN S 74 " (cutoff:3.500A) Processing helix chain 'S' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS S 125 " --> pdb=" O LEU S 121 " (cutoff:3.500A) Processing helix chain 'S' and resid 127 through 138 Processing helix chain 'S' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY S 160 " --> pdb=" O LEU S 156 " (cutoff:3.500A) Processing helix chain 'S' and resid 164 through 174 removed outlier: 3.762A pdb=" N GLU S 168 " --> pdb=" O SER S 164 " (cutoff:3.500A) Processing helix chain 'T' and resid -21 through -15 Processing helix chain 'T' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU T -8 " --> pdb=" O SER T -11 " (cutoff:3.500A) Processing helix chain 'T' and resid 14 through 42 Processing helix chain 'T' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY T 78 " --> pdb=" O GLN T 74 " (cutoff:3.500A) Processing helix chain 'T' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS T 125 " --> pdb=" O LEU T 121 " (cutoff:3.500A) Processing helix chain 'T' and resid 127 through 138 Processing helix chain 'T' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY T 160 " --> pdb=" O LEU T 156 " (cutoff:3.500A) Processing helix chain 'T' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU T 168 " --> pdb=" O SER T 164 " (cutoff:3.500A) Processing helix chain 'U' and resid -21 through -15 Processing helix chain 'U' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU U -8 " --> pdb=" O SER U -11 " (cutoff:3.500A) Processing helix chain 'U' and resid 14 through 42 Processing helix chain 'U' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY U 78 " --> pdb=" O GLN U 74 " (cutoff:3.500A) Processing helix chain 'U' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS U 125 " --> pdb=" O LEU U 121 " (cutoff:3.500A) Processing helix chain 'U' and resid 127 through 138 Processing helix chain 'U' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY U 160 " --> pdb=" O LEU U 156 " (cutoff:3.500A) Processing helix chain 'U' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU U 168 " --> pdb=" O SER U 164 " (cutoff:3.500A) Processing helix chain 'V' and resid -21 through -15 Processing helix chain 'V' and resid -13 through -8 removed outlier: 4.252A pdb=" N LEU V -8 " --> pdb=" O SER V -11 " (cutoff:3.500A) Processing helix chain 'V' and resid 14 through 42 Processing helix chain 'V' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY V 78 " --> pdb=" O GLN V 74 " (cutoff:3.500A) Processing helix chain 'V' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS V 125 " --> pdb=" O LEU V 121 " (cutoff:3.500A) Processing helix chain 'V' and resid 127 through 138 Processing helix chain 'V' and resid 138 through 160 removed outlier: 3.671A pdb=" N GLY V 160 " --> pdb=" O LEU V 156 " (cutoff:3.500A) Processing helix chain 'V' and resid 164 through 175 removed outlier: 3.763A pdb=" N GLU V 168 " --> pdb=" O SER V 164 " (cutoff:3.500A) Processing helix chain 'W' and resid -21 through -15 Processing helix chain 'W' and resid -13 through -8 removed outlier: 4.251A pdb=" N LEU W -8 " --> pdb=" O SER W -11 " (cutoff:3.500A) Processing helix chain 'W' and resid 14 through 42 Processing helix chain 'W' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY W 78 " --> pdb=" O GLN W 74 " (cutoff:3.500A) Processing helix chain 'W' and resid 96 through 125 removed outlier: 3.525A pdb=" N LYS W 125 " --> pdb=" O LEU W 121 " (cutoff:3.500A) Processing helix chain 'W' and resid 127 through 138 Processing helix chain 'W' and resid 138 through 160 removed outlier: 3.670A pdb=" N GLY W 160 " --> pdb=" O LEU W 156 " (cutoff:3.500A) Processing helix chain 'W' and resid 164 through 175 removed outlier: 3.762A pdb=" N GLU W 168 " --> pdb=" O SER W 164 " (cutoff:3.500A) Processing helix chain 'X' and resid -21 through -15 Processing helix chain 'X' and resid -13 through -8 removed outlier: 4.252A pdb=" N LEU X -8 " --> pdb=" O SER X -11 " (cutoff:3.500A) Processing helix chain 'X' and resid 14 through 42 Processing helix chain 'X' and resid 49 through 78 removed outlier: 3.501A pdb=" N GLY X 78 " --> pdb=" O GLN X 74 " (cutoff:3.500A) Processing helix chain 'X' and resid 96 through 125 removed outlier: 3.526A pdb=" N LYS X 125 " --> pdb=" O LEU X 121 " (cutoff:3.500A) Processing helix chain 'X' and resid 127 through 138 Processing helix chain 'X' and resid 138 through 160 removed outlier: 3.671A pdb=" N GLY X 160 " --> pdb=" O LEU X 156 " (cutoff:3.500A) Processing helix chain 'X' and resid 164 through 175 removed outlier: 3.763A pdb=" N GLU X 168 " --> pdb=" O SER X 164 " (cutoff:3.500A) 2712 hydrogen bonds defined for protein. 7992 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: 5.70 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 12520 1.34 - 1.46: 5320 1.46 - 1.58: 19744 1.58 - 1.69: 0 1.69 - 1.81: 264 Bond restraints: 37848 Sorted by residual: bond pdb=" N THR S 175 " pdb=" CA THR S 175 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.17e-02 7.31e+03 7.54e+00 bond pdb=" N THR H 175 " pdb=" CA THR H 175 " ideal model delta sigma weight residual 1.459 1.491 -0.032 1.18e-02 7.18e+03 7.17e+00 bond pdb=" N LYS S 173 " pdb=" CA LYS S 173 " ideal model delta sigma weight residual 1.458 1.490 -0.031 1.26e-02 6.30e+03 6.22e+00 bond pdb=" N HIS H 174 " pdb=" CA HIS H 174 " ideal model delta sigma weight residual 1.463 1.490 -0.027 1.08e-02 8.57e+03 6.11e+00 bond pdb=" N PHE H 171 " pdb=" CA PHE H 171 " ideal model delta sigma weight residual 1.459 1.488 -0.029 1.21e-02 6.83e+03 5.90e+00 ... (remaining 37843 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.42: 48948 1.42 - 2.83: 1677 2.83 - 4.25: 303 4.25 - 5.66: 24 5.66 - 7.08: 72 Bond angle restraints: 51024 Sorted by residual: angle pdb=" CA HIS H 174 " pdb=" C HIS H 174 " pdb=" O HIS H 174 " ideal model delta sigma weight residual 120.89 117.21 3.68 1.05e+00 9.07e-01 1.23e+01 angle pdb=" CA ASP H 172 " pdb=" CB ASP H 172 " pdb=" CG ASP H 172 " ideal model delta sigma weight residual 112.60 116.04 -3.44 1.00e+00 1.00e+00 1.18e+01 angle pdb=" N GLU G 95 " pdb=" CA GLU G 95 " pdb=" C GLU G 95 " ideal model delta sigma weight residual 110.80 117.88 -7.08 2.13e+00 2.20e-01 1.10e+01 angle pdb=" N GLU J 95 " pdb=" CA GLU J 95 " pdb=" C GLU J 95 " ideal model delta sigma weight residual 110.80 117.87 -7.07 2.13e+00 2.20e-01 1.10e+01 angle pdb=" N GLU Q 95 " pdb=" CA GLU Q 95 " pdb=" C GLU Q 95 " ideal model delta sigma weight residual 110.80 117.86 -7.06 2.13e+00 2.20e-01 1.10e+01 ... (remaining 51019 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 20321 17.92 - 35.83: 1896 35.83 - 53.75: 459 53.75 - 71.66: 123 71.66 - 89.58: 25 Dihedral angle restraints: 22824 sinusoidal: 9456 harmonic: 13368 Sorted by residual: dihedral pdb=" CA TRP I 94 " pdb=" C TRP I 94 " pdb=" N GLU I 95 " pdb=" CA GLU I 95 " ideal model delta harmonic sigma weight residual 180.00 162.93 17.07 0 5.00e+00 4.00e-02 1.17e+01 dihedral pdb=" CA ASP H 172 " pdb=" CB ASP H 172 " pdb=" CG ASP H 172 " pdb=" OD1 ASP H 172 " ideal model delta sinusoidal sigma weight residual -30.00 -89.02 59.02 1 2.00e+01 2.50e-03 1.16e+01 dihedral pdb=" CA TRP B 94 " pdb=" C TRP B 94 " pdb=" N GLU B 95 " pdb=" CA GLU B 95 " ideal model delta harmonic sigma weight residual 180.00 162.94 17.06 0 5.00e+00 4.00e-02 1.16e+01 ... (remaining 22821 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 2995 0.030 - 0.060: 1656 0.060 - 0.090: 519 0.090 - 0.120: 162 0.120 - 0.150: 68 Chirality restraints: 5400 Sorted by residual: chirality pdb=" CA TYR P 40 " pdb=" N TYR P 40 " pdb=" C TYR P 40 " pdb=" CB TYR P 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.63e-01 chirality pdb=" CA TYR X 40 " pdb=" N TYR X 40 " pdb=" C TYR X 40 " pdb=" CB TYR X 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA TYR B 40 " pdb=" N TYR B 40 " pdb=" C TYR B 40 " pdb=" CB TYR B 40 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.59e-01 ... (remaining 5397 not shown) Planarity restraints: 6696 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA O 167 " 0.009 2.00e-02 2.50e+03 1.93e-02 3.73e+00 pdb=" C ALA O 167 " -0.033 2.00e-02 2.50e+03 pdb=" O ALA O 167 " 0.013 2.00e-02 2.50e+03 pdb=" N GLU O 168 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR N 33 " -0.017 2.00e-02 2.50e+03 1.33e-02 3.53e+00 pdb=" CG TYR N 33 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR N 33 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR N 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR N 33 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR N 33 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR N 33 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR N 33 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR M 33 " -0.017 2.00e-02 2.50e+03 1.32e-02 3.50e+00 pdb=" CG TYR M 33 " 0.032 2.00e-02 2.50e+03 pdb=" CD1 TYR M 33 " -0.008 2.00e-02 2.50e+03 pdb=" CD2 TYR M 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR M 33 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR M 33 " -0.004 2.00e-02 2.50e+03 pdb=" CZ TYR M 33 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR M 33 " -0.003 2.00e-02 2.50e+03 ... (remaining 6693 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 10369 2.84 - 3.36: 35399 3.36 - 3.87: 60574 3.87 - 4.39: 68812 4.39 - 4.90: 116948 Nonbonded interactions: 292102 Sorted by model distance: nonbonded pdb=" OG1 THR J 175 " pdb=" OH TYR K 169 " model vdw 2.329 3.040 nonbonded pdb=" OD1 ASP G 85 " pdb=" N LYS H 88 " model vdw 2.357 3.120 nonbonded pdb=" OH TYR N 169 " pdb=" OG1 THR U 175 " model vdw 2.395 3.040 nonbonded pdb=" OG1 THR V 154 " pdb=" NE2 GLN X 8 " model vdw 2.418 3.120 nonbonded pdb=" OD1 ASP Q 85 " pdb=" N LYS R 88 " model vdw 2.458 3.120 ... (remaining 292097 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: 0.08 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' selection = chain 'P' selection = chain 'Q' selection = chain 'R' selection = chain 'S' selection = chain 'T' selection = chain 'U' selection = chain 'V' selection = chain 'W' selection = chain 'X' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.450 Check model and map are aligned: 0.080 Set scattering table: 0.080 Process input model: 26.590 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.100 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:6.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.510 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6925 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 37848 Z= 0.262 Angle : 0.687 7.079 51024 Z= 0.412 Chirality : 0.042 0.150 5400 Planarity : 0.004 0.028 6696 Dihedral : 15.691 89.575 14136 Min Nonbonded Distance : 2.329 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Rotamer: Outliers : 1.80 % Allowed : 4.22 % Favored : 93.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 3.30 (0.12), residues: 4416 helix: 2.84 (0.08), residues: 3312 sheet: None (None), residues: 0 loop : 0.09 (0.20), residues: 1104 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG I 23 TYR 0.032 0.003 TYR N 33 PHE 0.016 0.003 PHE H 42 TRP 0.005 0.001 TRP X 94 HIS 0.003 0.001 HIS L 14 Details of bonding type rmsd covalent geometry : bond 0.00457 (37848) covalent geometry : angle 0.68726 (51024) hydrogen bonds : bond 0.17101 ( 2712) hydrogen bonds : angle 4.38509 ( 7992) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 557 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 484 time to evaluate : 1.534 Fit side-chains REVERT: H 101 MET cc_start: 0.6757 (mmt) cc_final: 0.6464 (mmt) outliers start: 73 outliers final: 0 residues processed: 530 average time/residue: 0.9252 time to fit residues: 560.4075 Evaluate side-chains 285 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 285 time to evaluate : 1.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 197 optimal weight: 20.0000 chunk 388 optimal weight: 20.0000 chunk 215 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 3.9990 chunk 261 optimal weight: 9.9990 chunk 248 optimal weight: 9.9990 chunk 207 optimal weight: 6.9990 chunk 401 optimal weight: 10.0000 chunk 424 optimal weight: 20.0000 chunk 155 optimal weight: 8.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 11 GLN A 140 ASN B -15 ASN B 137 HIS B 140 ASN C 11 GLN C 140 ASN D 11 GLN D 140 ASN E 137 HIS E 140 ASN F 11 GLN F 140 ASN G 11 GLN G 140 ASN H 11 GLN H 140 ASN I 140 ASN J 137 HIS J 140 ASN K 11 GLN K 140 ASN L 140 ASN M 11 GLN M 140 ASN N 11 GLN N 140 ASN O 11 GLN O 140 ASN P 140 ASN Q 11 GLN Q 140 ASN R 11 GLN R 140 ASN S 11 GLN S 140 ASN T 11 GLN T 140 ASN U 11 GLN U 140 ASN V 140 ASN W 11 GLN W 140 ASN X 11 GLN X 140 ASN Total number of N/Q/H flips: 45 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.058980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2896 r_free = 0.2896 target = 0.049272 restraints weight = 127948.117| |-----------------------------------------------------------------------------| r_work (start): 0.2890 rms_B_bonded: 3.25 r_work: 0.2734 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.2734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9178 moved from start: 0.3052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 37848 Z= 0.194 Angle : 0.607 11.763 51024 Z= 0.322 Chirality : 0.038 0.147 5400 Planarity : 0.003 0.029 6696 Dihedral : 3.739 18.717 4848 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 1.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.48 % Allowed : 8.26 % Favored : 90.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.13 (0.12), residues: 4416 helix: 4.11 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : 0.62 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG F 64 TYR 0.018 0.002 TYR E 40 PHE 0.013 0.002 PHE P 133 TRP 0.009 0.002 TRP B 94 HIS 0.004 0.001 HIS E 119 Details of bonding type rmsd covalent geometry : bond 0.00410 (37848) covalent geometry : angle 0.60722 (51024) hydrogen bonds : bond 0.09193 ( 2712) hydrogen bonds : angle 3.76249 ( 7992) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 305 time to evaluate : 1.387 Fit side-chains REVERT: D -10 GLU cc_start: 0.8668 (mp0) cc_final: 0.8466 (mp0) REVERT: D 64 ARG cc_start: 0.9122 (OUTLIER) cc_final: 0.8821 (ttm-80) REVERT: F -10 GLU cc_start: 0.8594 (mp0) cc_final: 0.8369 (mp0) REVERT: O -10 GLU cc_start: 0.8549 (mp0) cc_final: 0.8316 (mp0) REVERT: W 64 ARG cc_start: 0.9050 (OUTLIER) cc_final: 0.8601 (ttm170) REVERT: X 64 ARG cc_start: 0.9057 (tpp80) cc_final: 0.8612 (tpp80) outliers start: 60 outliers final: 0 residues processed: 357 average time/residue: 0.7642 time to fit residues: 320.4106 Evaluate side-chains 278 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 276 time to evaluate : 1.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 64 ARG Chi-restraints excluded: chain W residue 64 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 160 optimal weight: 9.9990 chunk 409 optimal weight: 20.0000 chunk 163 optimal weight: 5.9990 chunk 255 optimal weight: 10.0000 chunk 315 optimal weight: 8.9990 chunk 416 optimal weight: 20.0000 chunk 428 optimal weight: 7.9990 chunk 343 optimal weight: 0.7980 chunk 51 optimal weight: 9.9990 chunk 377 optimal weight: 9.9990 chunk 346 optimal weight: 9.9990 overall best weight: 6.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 11 GLN E 11 GLN I 11 GLN J 11 GLN L 11 GLN P 11 GLN V 11 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3096 r_free = 0.3096 target = 0.057506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2863 r_free = 0.2863 target = 0.047632 restraints weight = 126622.082| |-----------------------------------------------------------------------------| r_work (start): 0.2863 rms_B_bonded: 3.30 r_work: 0.2701 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2701 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9210 moved from start: 0.3486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 37848 Z= 0.196 Angle : 0.596 10.872 51024 Z= 0.314 Chirality : 0.038 0.137 5400 Planarity : 0.003 0.033 6696 Dihedral : 3.581 18.365 4848 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 1.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 1.26 % Allowed : 9.20 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.41 (0.12), residues: 4416 helix: 4.35 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : 0.54 (0.21), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG T 64 TYR 0.018 0.002 TYR J 40 PHE 0.010 0.002 PHE I 133 TRP 0.007 0.001 TRP I 94 HIS 0.004 0.001 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00420 (37848) covalent geometry : angle 0.59597 (51024) hydrogen bonds : bond 0.09458 ( 2712) hydrogen bonds : angle 3.70728 ( 7992) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 341 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 290 time to evaluate : 1.291 Fit side-chains REVERT: F -10 GLU cc_start: 0.8493 (mp0) cc_final: 0.8233 (mp0) REVERT: R 64 ARG cc_start: 0.9141 (OUTLIER) cc_final: 0.8890 (ttt90) REVERT: V 64 ARG cc_start: 0.9128 (OUTLIER) cc_final: 0.8822 (ttt90) outliers start: 51 outliers final: 1 residues processed: 307 average time/residue: 0.7925 time to fit residues: 284.3695 Evaluate side-chains 282 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 279 time to evaluate : 1.198 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -11 SER Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain V residue 64 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 28 optimal weight: 0.3980 chunk 100 optimal weight: 20.0000 chunk 354 optimal weight: 10.0000 chunk 76 optimal weight: 5.9990 chunk 121 optimal weight: 8.9990 chunk 376 optimal weight: 10.0000 chunk 319 optimal weight: 8.9990 chunk 288 optimal weight: 40.0000 chunk 292 optimal weight: 9.9990 chunk 143 optimal weight: 0.1980 chunk 117 optimal weight: 9.9990 overall best weight: 4.9186 ------------------------------------------------------------------------------- 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 = 0.3142 r_free = 0.3142 target = 0.059098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2915 r_free = 0.2915 target = 0.049578 restraints weight = 127124.478| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 3.21 r_work: 0.2753 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2753 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9168 moved from start: 0.3756 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 37848 Z= 0.158 Angle : 0.554 10.977 51024 Z= 0.291 Chirality : 0.036 0.133 5400 Planarity : 0.003 0.034 6696 Dihedral : 3.505 17.535 4848 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 1.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.84 % Allowed : 10.36 % Favored : 88.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.70 (0.12), residues: 4416 helix: 4.68 (0.08), residues: 3384 sheet: None (None), residues: 0 loop : 0.26 (0.20), residues: 1032 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG X 64 TYR 0.018 0.001 TYR G 40 PHE 0.012 0.001 PHE B -20 TRP 0.007 0.001 TRP R 94 HIS 0.004 0.000 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00324 (37848) covalent geometry : angle 0.55409 (51024) hydrogen bonds : bond 0.08111 ( 2712) hydrogen bonds : angle 3.39482 ( 7992) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 301 time to evaluate : 1.402 Fit side-chains REVERT: H -10 GLU cc_start: 0.8580 (mp0) cc_final: 0.8367 (pm20) REVERT: Q -10 GLU cc_start: 0.8608 (mp0) cc_final: 0.8378 (pm20) REVERT: R 64 ARG cc_start: 0.9142 (OUTLIER) cc_final: 0.8935 (ttt90) REVERT: V 64 ARG cc_start: 0.9067 (OUTLIER) cc_final: 0.8854 (ttt90) outliers start: 34 outliers final: 1 residues processed: 308 average time/residue: 0.7905 time to fit residues: 286.2265 Evaluate side-chains 280 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 277 time to evaluate : 1.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 72 LYS Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain V residue 64 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 306 optimal weight: 40.0000 chunk 212 optimal weight: 7.9990 chunk 169 optimal weight: 20.0000 chunk 99 optimal weight: 7.9990 chunk 398 optimal weight: 3.9990 chunk 13 optimal weight: 5.9990 chunk 173 optimal weight: 20.0000 chunk 156 optimal weight: 9.9990 chunk 286 optimal weight: 10.0000 chunk 192 optimal weight: 10.0000 chunk 425 optimal weight: 10.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 HIS D 137 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2857 r_free = 0.2857 target = 0.047232 restraints weight = 126563.160| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 3.31 r_work: 0.2687 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.2687 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9221 moved from start: 0.3728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 37848 Z= 0.204 Angle : 0.582 10.998 51024 Z= 0.309 Chirality : 0.037 0.131 5400 Planarity : 0.003 0.033 6696 Dihedral : 3.517 17.649 4848 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 2.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.46 % Favored : 96.54 % Rotamer: Outliers : 0.99 % Allowed : 10.36 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.45 (0.12), residues: 4416 helix: 4.46 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : 0.21 (0.20), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 64 TYR 0.022 0.002 TYR G 40 PHE 0.009 0.002 PHE I 133 TRP 0.005 0.001 TRP V 94 HIS 0.004 0.001 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00444 (37848) covalent geometry : angle 0.58233 (51024) hydrogen bonds : bond 0.09352 ( 2712) hydrogen bonds : angle 3.66617 ( 7992) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 293 time to evaluate : 1.269 Fit side-chains REVERT: H -10 GLU cc_start: 0.8495 (mp0) cc_final: 0.8231 (mp0) REVERT: N 159 MET cc_start: 0.9205 (OUTLIER) cc_final: 0.8969 (mtp) REVERT: O -10 GLU cc_start: 0.8526 (mp0) cc_final: 0.8264 (mp0) REVERT: Q -10 GLU cc_start: 0.8508 (mp0) cc_final: 0.8221 (mp0) REVERT: R 64 ARG cc_start: 0.9167 (OUTLIER) cc_final: 0.8960 (ttt90) REVERT: V 64 ARG cc_start: 0.9096 (OUTLIER) cc_final: 0.8882 (ttt90) outliers start: 40 outliers final: 1 residues processed: 300 average time/residue: 0.7827 time to fit residues: 275.5064 Evaluate side-chains 284 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 280 time to evaluate : 1.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 MET Chi-restraints excluded: chain O residue -11 SER Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain V residue 64 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 29 optimal weight: 10.0000 chunk 279 optimal weight: 20.0000 chunk 55 optimal weight: 0.4980 chunk 188 optimal weight: 5.9990 chunk 418 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 268 optimal weight: 9.9990 chunk 82 optimal weight: 20.0000 chunk 89 optimal weight: 20.0000 chunk 341 optimal weight: 20.0000 chunk 390 optimal weight: 10.0000 overall best weight: 6.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.057442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2866 r_free = 0.2866 target = 0.047568 restraints weight = 126496.586| |-----------------------------------------------------------------------------| r_work (start): 0.2861 rms_B_bonded: 3.31 r_work: 0.2698 rms_B_bonded: 4.12 restraints_weight: 0.5000 r_work (final): 0.2698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9213 moved from start: 0.3797 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 37848 Z= 0.193 Angle : 0.576 11.056 51024 Z= 0.305 Chirality : 0.037 0.133 5400 Planarity : 0.003 0.033 6696 Dihedral : 3.496 17.101 4848 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 1.06 % Allowed : 10.31 % Favored : 88.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.50 (0.12), residues: 4416 helix: 4.51 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : 0.14 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG T 64 TYR 0.020 0.002 TYR G 40 PHE 0.009 0.002 PHE I 133 TRP 0.006 0.001 TRP M 94 HIS 0.003 0.000 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00418 (37848) covalent geometry : angle 0.57598 (51024) hydrogen bonds : bond 0.09014 ( 2712) hydrogen bonds : angle 3.58778 ( 7992) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 286 time to evaluate : 1.304 Fit side-chains REVERT: N 159 MET cc_start: 0.9251 (OUTLIER) cc_final: 0.8941 (mtp) REVERT: R 64 ARG cc_start: 0.9165 (OUTLIER) cc_final: 0.8964 (ttt90) REVERT: V 64 ARG cc_start: 0.9091 (OUTLIER) cc_final: 0.8888 (ttt90) outliers start: 43 outliers final: 1 residues processed: 293 average time/residue: 0.7688 time to fit residues: 265.8771 Evaluate side-chains 273 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 269 time to evaluate : 1.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -11 SER Chi-restraints excluded: chain N residue 159 MET Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain V residue 64 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 284 optimal weight: 8.9990 chunk 91 optimal weight: 9.9990 chunk 237 optimal weight: 6.9990 chunk 232 optimal weight: 8.9990 chunk 52 optimal weight: 10.0000 chunk 147 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 53 optimal weight: 20.0000 chunk 6 optimal weight: 9.9990 chunk 287 optimal weight: 6.9990 chunk 133 optimal weight: 7.9990 overall best weight: 6.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 137 HIS O 137 HIS Q 137 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3098 r_free = 0.3098 target = 0.057402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.047400 restraints weight = 126674.827| |-----------------------------------------------------------------------------| r_work (start): 0.2864 rms_B_bonded: 3.39 r_work: 0.2697 rms_B_bonded: 4.21 restraints_weight: 0.5000 r_work (final): 0.2697 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9218 moved from start: 0.3838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 37848 Z= 0.191 Angle : 0.576 11.038 51024 Z= 0.305 Chirality : 0.037 0.132 5400 Planarity : 0.003 0.033 6696 Dihedral : 3.491 16.978 4848 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 0.89 % Allowed : 11.00 % Favored : 88.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.51 (0.12), residues: 4416 helix: 4.51 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : 0.16 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG J 64 TYR 0.019 0.002 TYR G 40 PHE 0.010 0.002 PHE Q -20 TRP 0.007 0.001 TRP O -9 HIS 0.003 0.000 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00413 (37848) covalent geometry : angle 0.57615 (51024) hydrogen bonds : bond 0.08960 ( 2712) hydrogen bonds : angle 3.56494 ( 7992) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 316 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 280 time to evaluate : 1.329 Fit side-chains REVERT: F -10 GLU cc_start: 0.8125 (tm-30) cc_final: 0.7888 (pp20) REVERT: H -10 GLU cc_start: 0.8502 (mp0) cc_final: 0.8275 (pm20) REVERT: N 159 MET cc_start: 0.9247 (OUTLIER) cc_final: 0.8942 (mtp) REVERT: Q -10 GLU cc_start: 0.8495 (mp0) cc_final: 0.8282 (pm20) REVERT: R 64 ARG cc_start: 0.9164 (OUTLIER) cc_final: 0.8912 (ttm-80) REVERT: V 64 ARG cc_start: 0.9060 (OUTLIER) cc_final: 0.8801 (ttm-80) outliers start: 36 outliers final: 2 residues processed: 287 average time/residue: 0.7217 time to fit residues: 245.3922 Evaluate side-chains 264 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 259 time to evaluate : 1.300 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -11 SER Chi-restraints excluded: chain N residue 159 MET Chi-restraints excluded: chain O residue -11 SER Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain V residue 64 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 253 optimal weight: 10.0000 chunk 192 optimal weight: 9.9990 chunk 221 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 chunk 295 optimal weight: 9.9990 chunk 201 optimal weight: 9.9990 chunk 228 optimal weight: 10.0000 chunk 338 optimal weight: 9.9990 chunk 177 optimal weight: 0.9990 chunk 245 optimal weight: 9.9990 chunk 119 optimal weight: 10.0000 overall best weight: 5.3588 ------------------------------------------------------------------------------- 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 = 0.3126 r_free = 0.3126 target = 0.058540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2897 r_free = 0.2897 target = 0.048836 restraints weight = 125389.300| |-----------------------------------------------------------------------------| r_work (start): 0.2893 rms_B_bonded: 3.22 r_work: 0.2736 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2736 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9181 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 37848 Z= 0.166 Angle : 0.558 10.963 51024 Z= 0.294 Chirality : 0.036 0.131 5400 Planarity : 0.003 0.034 6696 Dihedral : 3.457 16.601 4848 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 0.17 % Allowed : 12.15 % Favored : 87.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.66 (0.12), residues: 4416 helix: 4.62 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : 0.25 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 64 TYR 0.018 0.001 TYR G 40 PHE 0.009 0.002 PHE I 133 TRP 0.007 0.001 TRP O 94 HIS 0.003 0.000 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00348 (37848) covalent geometry : angle 0.55772 (51024) hydrogen bonds : bond 0.08286 ( 2712) hydrogen bonds : angle 3.39321 ( 7992) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 268 time to evaluate : 1.192 Fit side-chains REVERT: G -10 GLU cc_start: 0.8321 (pm20) cc_final: 0.8108 (pm20) REVERT: H -10 GLU cc_start: 0.8415 (mp0) cc_final: 0.8198 (pm20) REVERT: N 159 MET cc_start: 0.9193 (OUTLIER) cc_final: 0.8920 (mtp) REVERT: Q -10 GLU cc_start: 0.8406 (mp0) cc_final: 0.8195 (pm20) REVERT: R 64 ARG cc_start: 0.9163 (OUTLIER) cc_final: 0.8876 (ttm-80) REVERT: V 64 ARG cc_start: 0.9062 (OUTLIER) cc_final: 0.8744 (ttm-80) outliers start: 7 outliers final: 2 residues processed: 271 average time/residue: 0.7050 time to fit residues: 226.9034 Evaluate side-chains 263 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 258 time to evaluate : 1.523 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -11 SER Chi-restraints excluded: chain N residue 159 MET Chi-restraints excluded: chain R residue 64 ARG Chi-restraints excluded: chain S residue 72 LYS Chi-restraints excluded: chain V residue 64 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 320 optimal weight: 10.0000 chunk 188 optimal weight: 10.0000 chunk 332 optimal weight: 5.9990 chunk 185 optimal weight: 7.9990 chunk 63 optimal weight: 9.9990 chunk 187 optimal weight: 10.0000 chunk 170 optimal weight: 10.0000 chunk 146 optimal weight: 0.5980 chunk 140 optimal weight: 9.9990 chunk 226 optimal weight: 7.9990 chunk 362 optimal weight: 6.9990 overall best weight: 5.9188 ------------------------------------------------------------------------------- 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 = 0.3115 r_free = 0.3115 target = 0.058115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.048347 restraints weight = 126531.043| |-----------------------------------------------------------------------------| r_work (start): 0.2881 rms_B_bonded: 3.26 r_work: 0.2722 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9193 moved from start: 0.3914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.022 37848 Z= 0.177 Angle : 0.559 10.950 51024 Z= 0.296 Chirality : 0.037 0.143 5400 Planarity : 0.003 0.034 6696 Dihedral : 3.465 16.682 4848 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 0.27 % Allowed : 12.40 % Favored : 87.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.57 (0.12), residues: 4416 helix: 4.56 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : 0.17 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG J 64 TYR 0.018 0.002 TYR G 40 PHE 0.009 0.002 PHE I 133 TRP 0.006 0.001 TRP Q 94 HIS 0.003 0.000 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00375 (37848) covalent geometry : angle 0.55947 (51024) hydrogen bonds : bond 0.08571 ( 2712) hydrogen bonds : angle 3.45151 ( 7992) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 265 time to evaluate : 1.605 Fit side-chains REVERT: G -10 GLU cc_start: 0.8350 (pm20) cc_final: 0.8128 (pm20) REVERT: H -10 GLU cc_start: 0.8449 (mp0) cc_final: 0.8236 (pm20) REVERT: N 159 MET cc_start: 0.9216 (OUTLIER) cc_final: 0.8957 (mtp) REVERT: Q -10 GLU cc_start: 0.8433 (mp0) cc_final: 0.8221 (pm20) outliers start: 11 outliers final: 1 residues processed: 268 average time/residue: 0.7048 time to fit residues: 225.9885 Evaluate side-chains 261 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 259 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -11 SER Chi-restraints excluded: chain N residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 378 optimal weight: 40.0000 chunk 132 optimal weight: 10.0000 chunk 194 optimal weight: 6.9990 chunk 346 optimal weight: 10.0000 chunk 3 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 216 optimal weight: 40.0000 chunk 210 optimal weight: 9.9990 chunk 278 optimal weight: 9.9990 chunk 323 optimal weight: 8.9990 chunk 268 optimal weight: 10.0000 overall best weight: 8.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** I 137 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** X 137 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.056387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.046246 restraints weight = 127011.245| |-----------------------------------------------------------------------------| r_work (start): 0.2828 rms_B_bonded: 3.36 r_work: 0.2661 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.2661 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9246 moved from start: 0.3806 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 37848 Z= 0.244 Angle : 0.610 11.056 51024 Z= 0.325 Chirality : 0.039 0.164 5400 Planarity : 0.003 0.035 6696 Dihedral : 3.552 16.880 4848 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.07 % Allowed : 12.57 % Favored : 87.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.18 (0.12), residues: 4416 helix: 4.31 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : -0.08 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 64 TYR 0.020 0.002 TYR G 40 PHE 0.009 0.002 PHE E 42 TRP 0.006 0.001 TRP P -9 HIS 0.004 0.001 HIS V 66 Details of bonding type rmsd covalent geometry : bond 0.00546 (37848) covalent geometry : angle 0.60970 (51024) hydrogen bonds : bond 0.10001 ( 2712) hydrogen bonds : angle 3.80639 ( 7992) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 8832 Ramachandran restraints generated. 4416 Oldfield, 0 Emsley, 4416 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 265 time to evaluate : 1.015 Fit side-chains REVERT: H -10 GLU cc_start: 0.8480 (mp0) cc_final: 0.8210 (mp0) REVERT: N 159 MET cc_start: 0.9303 (OUTLIER) cc_final: 0.9043 (mtp) REVERT: O -10 GLU cc_start: 0.8315 (pp20) cc_final: 0.8055 (pp20) REVERT: Q -10 GLU cc_start: 0.8448 (mp0) cc_final: 0.8239 (pm20) outliers start: 3 outliers final: 0 residues processed: 265 average time/residue: 0.7326 time to fit residues: 231.7323 Evaluate side-chains 254 residues out of total 4056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 253 time to evaluate : 1.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain N residue 159 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 432 random chunks: chunk 425 optimal weight: 3.9990 chunk 268 optimal weight: 9.9990 chunk 115 optimal weight: 10.0000 chunk 344 optimal weight: 9.9990 chunk 309 optimal weight: 5.9990 chunk 320 optimal weight: 2.9990 chunk 150 optimal weight: 9.9990 chunk 222 optimal weight: 9.9990 chunk 401 optimal weight: 4.9990 chunk 77 optimal weight: 6.9990 chunk 13 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 119 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.060320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2943 r_free = 0.2943 target = 0.050623 restraints weight = 126009.684| |-----------------------------------------------------------------------------| r_work (start): 0.2934 rms_B_bonded: 3.29 r_work: 0.2782 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9144 moved from start: 0.4078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 37848 Z= 0.141 Angle : 0.549 10.913 51024 Z= 0.288 Chirality : 0.036 0.153 5400 Planarity : 0.003 0.035 6696 Dihedral : 3.430 16.347 4848 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 0.17 % Allowed : 12.77 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 25.00 % 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 aren not related in a simple way. whole: 5.75 (0.12), residues: 4416 helix: 4.75 (0.08), residues: 3408 sheet: None (None), residues: 0 loop : 0.00 (0.19), residues: 1008 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG T 64 TYR 0.018 0.001 TYR G 40 PHE 0.009 0.001 PHE C -20 TRP 0.008 0.001 TRP Q 94 HIS 0.003 0.000 HIS P 137 Details of bonding type rmsd covalent geometry : bond 0.00284 (37848) covalent geometry : angle 0.54918 (51024) hydrogen bonds : bond 0.07269 ( 2712) hydrogen bonds : angle 3.16153 ( 7992) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 10592.97 seconds wall clock time: 181 minutes 19.16 seconds (10879.16 seconds total)