Starting phenix.real_space_refine on Fri Aug 22 14:24:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az5_15754/08_2025/8az5_15754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az5_15754/08_2025/8az5_15754.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8az5_15754/08_2025/8az5_15754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az5_15754/08_2025/8az5_15754.map" model { file = "/net/cci-nas-00/data/ceres_data/8az5_15754/08_2025/8az5_15754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az5_15754/08_2025/8az5_15754.cif" } resolution = 2.3 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= 0.000 sd= 0.003 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: 3 Type Number sf(0) Gaussians C 2500 2.51 5 N 760 2.21 5 O 800 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 60 residue(s): 0.01s 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: 4060 Number of models: 1 Model: "" Number of chains: 53 Chain: "A" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "P" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "Q" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "Q" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "R" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "R" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "S" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "S" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "T" Number of atoms: 201 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 201 Classifications: {'peptide': 27} Link IDs: {'TRANS': 26} Chain: "T" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "I" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "J" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "N" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Chain: "Q" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Chain: "R" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 0.94, per 1000 atoms: 0.23 Number of scatterers: 4060 At special positions: 0 Unit cell: (90, 103.5, 42.3, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 800 8.00 N 760 7.00 C 2500 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=20, symmetry=0 Number of additional bonds: simple=20, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.32 Conformation dependent library (CDL) restraints added in 131.3 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 960 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 14 sheets defined 0.0% alpha, 53.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 12 through 19 removed outlier: 6.771A pdb=" N ALA E 13 " --> pdb=" O ASN I 14 " (cutoff:3.500A) removed outlier: 8.046A pdb=" N LEU I 16 " --> pdb=" O ALA E 13 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N PHE E 15 " --> pdb=" O LEU I 16 " (cutoff:3.500A) removed outlier: 7.747A pdb=" N HIS I 18 " --> pdb=" O PHE E 15 " (cutoff:3.500A) removed outlier: 6.548A pdb=" N VAL E 17 " --> pdb=" O HIS I 18 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 22 through 27 removed outlier: 7.006A pdb=" N ALA E 25 " --> pdb=" O GLY A 24 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE A 26 " --> pdb=" O ALA E 25 " (cutoff:3.500A) removed outlier: 7.179A pdb=" N LEU E 27 " --> pdb=" O ILE A 26 " (cutoff:3.500A) removed outlier: 6.624A pdb=" N PHE E 23 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 8.128A pdb=" N ILE I 26 " --> pdb=" O PHE E 23 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N ALA E 25 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ALA M 25 " --> pdb=" O GLY I 24 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ILE I 26 " --> pdb=" O ALA M 25 " (cutoff:3.500A) removed outlier: 6.796A pdb=" N LEU M 27 " --> pdb=" O ILE I 26 " (cutoff:3.500A) removed outlier: 6.729A pdb=" N ALA Q 25 " --> pdb=" O GLY M 24 " (cutoff:3.500A) removed outlier: 6.954A pdb=" N ILE M 26 " --> pdb=" O ALA Q 25 " (cutoff:3.500A) removed outlier: 6.956A pdb=" N LEU Q 27 " --> pdb=" O ILE M 26 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 30 through 32 removed outlier: 8.559A pdb=" N THR A 30 " --> pdb=" O ASN E 31 " (cutoff:3.500A) removed outlier: 8.618A pdb=" N THR E 30 " --> pdb=" O ASN I 31 " (cutoff:3.500A) removed outlier: 8.524A pdb=" N THR I 30 " --> pdb=" O ASN M 31 " (cutoff:3.500A) removed outlier: 8.506A pdb=" N THR M 30 " --> pdb=" O ASN Q 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 35 through 36 Processing sheet with id=AA5, first strand: chain 'B' and resid 12 through 19 removed outlier: 6.819A pdb=" N ALA F 13 " --> pdb=" O ASN J 14 " (cutoff:3.500A) removed outlier: 8.094A pdb=" N LEU J 16 " --> pdb=" O ALA F 13 " (cutoff:3.500A) removed outlier: 6.353A pdb=" N PHE F 15 " --> pdb=" O LEU J 16 " (cutoff:3.500A) removed outlier: 7.771A pdb=" N HIS J 18 " --> pdb=" O PHE F 15 " (cutoff:3.500A) removed outlier: 6.570A pdb=" N VAL F 17 " --> pdb=" O HIS J 18 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 22 through 27 removed outlier: 6.844A pdb=" N ALA F 25 " --> pdb=" O GLY B 24 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N ILE B 26 " --> pdb=" O ALA F 25 " (cutoff:3.500A) removed outlier: 7.033A pdb=" N LEU F 27 " --> pdb=" O ILE B 26 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N PHE F 23 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 8.228A pdb=" N ILE J 26 " --> pdb=" O PHE F 23 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N ALA F 25 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ALA N 25 " --> pdb=" O GLY J 24 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N ILE J 26 " --> pdb=" O ALA N 25 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N LEU N 27 " --> pdb=" O ILE J 26 " (cutoff:3.500A) removed outlier: 6.737A pdb=" N ALA R 25 " --> pdb=" O GLY N 24 " (cutoff:3.500A) removed outlier: 6.950A pdb=" N ILE N 26 " --> pdb=" O ALA R 25 " (cutoff:3.500A) removed outlier: 6.949A pdb=" N LEU R 27 " --> pdb=" O ILE N 26 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 30 through 32 removed outlier: 8.548A pdb=" N THR B 30 " --> pdb=" O ASN F 31 " (cutoff:3.500A) removed outlier: 8.666A pdb=" N THR F 30 " --> pdb=" O ASN J 31 " (cutoff:3.500A) removed outlier: 8.468A pdb=" N THR J 30 " --> pdb=" O ASN N 31 " (cutoff:3.500A) removed outlier: 8.508A pdb=" N THR N 30 " --> pdb=" O ASN R 31 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 35 through 36 Processing sheet with id=AA9, first strand: chain 'C' and resid 12 through 18 removed outlier: 6.617A pdb=" N LEU G 12 " --> pdb=" O ALA K 13 " (cutoff:3.500A) removed outlier: 7.903A pdb=" N PHE K 15 " --> pdb=" O LEU G 12 " (cutoff:3.500A) removed outlier: 6.342A pdb=" N ASN G 14 " --> pdb=" O PHE K 15 " (cutoff:3.500A) removed outlier: 7.723A pdb=" N VAL K 17 " --> pdb=" O ASN G 14 " (cutoff:3.500A) removed outlier: 6.361A pdb=" N LEU G 16 " --> pdb=" O VAL K 17 " (cutoff:3.500A) removed outlier: 6.300A pdb=" N LEU K 12 " --> pdb=" O ALA O 13 " (cutoff:3.500A) removed outlier: 7.650A pdb=" N PHE O 15 " --> pdb=" O LEU K 12 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N ASN K 14 " --> pdb=" O PHE O 15 " (cutoff:3.500A) removed outlier: 7.505A pdb=" N VAL O 17 " --> pdb=" O ASN K 14 " (cutoff:3.500A) removed outlier: 6.141A pdb=" N LEU K 16 " --> pdb=" O VAL O 17 " (cutoff:3.500A) removed outlier: 6.474A pdb=" N LEU O 12 " --> pdb=" O ALA S 13 " (cutoff:3.500A) removed outlier: 7.835A pdb=" N PHE S 15 " --> pdb=" O LEU O 12 " (cutoff:3.500A) removed outlier: 6.184A pdb=" N ASN O 14 " --> pdb=" O PHE S 15 " (cutoff:3.500A) removed outlier: 7.614A pdb=" N VAL S 17 " --> pdb=" O ASN O 14 " (cutoff:3.500A) removed outlier: 6.252A pdb=" N LEU O 16 " --> pdb=" O VAL S 17 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 25 through 32 Processing sheet with id=AB2, first strand: chain 'C' and resid 35 through 36 removed outlier: 6.182A pdb=" N ASN C 35 " --> pdb=" O THR G 36 " (cutoff:3.500A) removed outlier: 6.085A pdb=" N ASN G 35 " --> pdb=" O THR K 36 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN K 35 " --> pdb=" O THR O 36 " (cutoff:3.500A) removed outlier: 6.227A pdb=" N ASN O 35 " --> pdb=" O THR S 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'D' and resid 12 through 18 removed outlier: 6.687A pdb=" N LEU D 12 " --> pdb=" O ALA H 13 " (cutoff:3.500A) removed outlier: 7.986A pdb=" N PHE H 15 " --> pdb=" O LEU D 12 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N ASN D 14 " --> pdb=" O PHE H 15 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N VAL H 17 " --> pdb=" O ASN D 14 " (cutoff:3.500A) removed outlier: 6.392A pdb=" N LEU D 16 " --> pdb=" O VAL H 17 " (cutoff:3.500A) removed outlier: 6.666A pdb=" N LEU H 12 " --> pdb=" O ALA L 13 " (cutoff:3.500A) removed outlier: 7.956A pdb=" N PHE L 15 " --> pdb=" O LEU H 12 " (cutoff:3.500A) removed outlier: 6.394A pdb=" N ASN H 14 " --> pdb=" O PHE L 15 " (cutoff:3.500A) removed outlier: 7.761A pdb=" N VAL L 17 " --> pdb=" O ASN H 14 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N LEU H 16 " --> pdb=" O VAL L 17 " (cutoff:3.500A) removed outlier: 6.292A pdb=" N LEU L 12 " --> pdb=" O ALA P 13 " (cutoff:3.500A) removed outlier: 7.644A pdb=" N PHE P 15 " --> pdb=" O LEU L 12 " (cutoff:3.500A) removed outlier: 6.054A pdb=" N ASN L 14 " --> pdb=" O PHE P 15 " (cutoff:3.500A) removed outlier: 7.483A pdb=" N VAL P 17 " --> pdb=" O ASN L 14 " (cutoff:3.500A) removed outlier: 6.108A pdb=" N LEU L 16 " --> pdb=" O VAL P 17 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU P 12 " --> pdb=" O ALA T 13 " (cutoff:3.500A) removed outlier: 7.826A pdb=" N PHE T 15 " --> pdb=" O LEU P 12 " (cutoff:3.500A) removed outlier: 6.176A pdb=" N ASN P 14 " --> pdb=" O PHE T 15 " (cutoff:3.500A) removed outlier: 7.603A pdb=" N VAL T 17 " --> pdb=" O ASN P 14 " (cutoff:3.500A) removed outlier: 6.244A pdb=" N LEU P 16 " --> pdb=" O VAL T 17 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'D' and resid 26 through 32 removed outlier: 6.495A pdb=" N ILE H 26 " --> pdb=" O LEU L 27 " (cutoff:3.500A) removed outlier: 8.218A pdb=" N SER L 29 " --> pdb=" O ILE H 26 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N SER H 28 " --> pdb=" O SER L 29 " (cutoff:3.500A) removed outlier: 8.363A pdb=" N ASN L 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 6.510A pdb=" N THR H 30 " --> pdb=" O ASN L 31 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 35 through 36 removed outlier: 6.242A pdb=" N ASN D 35 " --> pdb=" O THR H 36 " (cutoff:3.500A) removed outlier: 6.282A pdb=" N ASN H 35 " --> pdb=" O THR L 36 " (cutoff:3.500A) removed outlier: 6.243A pdb=" N ASN L 35 " --> pdb=" O THR P 36 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N ASN P 35 " --> pdb=" O THR T 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 115 hydrogen bonds defined for protein. 342 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: 0.38 Time building geometry restraints manager: 0.40 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 640 1.28 - 1.35: 720 1.35 - 1.41: 461 1.41 - 1.48: 667 1.48 - 1.54: 1592 Bond restraints: 4080 Sorted by residual: bond pdb=" CB VAL P 32 " pdb=" CG2 VAL P 32 " ideal model delta sigma weight residual 1.521 1.472 0.049 3.30e-02 9.18e+02 2.23e+00 bond pdb=" CB VAL O 32 " pdb=" CG2 VAL O 32 " ideal model delta sigma weight residual 1.521 1.473 0.048 3.30e-02 9.18e+02 2.14e+00 bond pdb=" CB VAL H 32 " pdb=" CG2 VAL H 32 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.93e+00 bond pdb=" CB VAL D 32 " pdb=" CG2 VAL D 32 " ideal model delta sigma weight residual 1.521 1.475 0.046 3.30e-02 9.18e+02 1.91e+00 bond pdb=" CB VAL K 32 " pdb=" CG2 VAL K 32 " ideal model delta sigma weight residual 1.521 1.476 0.045 3.30e-02 9.18e+02 1.90e+00 ... (remaining 4075 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.01: 5001 1.01 - 2.02: 415 2.02 - 3.03: 64 3.03 - 4.04: 30 4.04 - 5.05: 10 Bond angle restraints: 5520 Sorted by residual: angle pdb=" C VAL H 32 " pdb=" N GLY H 33 " pdb=" CA GLY H 33 " ideal model delta sigma weight residual 120.11 123.44 -3.33 1.51e+00 4.39e-01 4.87e+00 angle pdb=" N GLY O 33 " pdb=" CA GLY O 33 " pdb=" C GLY O 33 " ideal model delta sigma weight residual 113.48 116.70 -3.22 1.46e+00 4.69e-01 4.86e+00 angle pdb=" C VAL L 32 " pdb=" N GLY L 33 " pdb=" CA GLY L 33 " ideal model delta sigma weight residual 120.11 123.44 -3.33 1.51e+00 4.39e-01 4.86e+00 angle pdb=" C VAL G 32 " pdb=" N GLY G 33 " pdb=" CA GLY G 33 " ideal model delta sigma weight residual 120.11 123.43 -3.32 1.51e+00 4.39e-01 4.82e+00 angle pdb=" C VAL D 32 " pdb=" N GLY D 33 " pdb=" CA GLY D 33 " ideal model delta sigma weight residual 120.11 123.41 -3.30 1.51e+00 4.39e-01 4.78e+00 ... (remaining 5515 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.87: 1849 8.87 - 17.75: 291 17.75 - 26.62: 83 26.62 - 35.50: 37 35.50 - 44.37: 20 Dihedral angle restraints: 2280 sinusoidal: 780 harmonic: 1500 Sorted by residual: dihedral pdb=" CA LEU E 16 " pdb=" C LEU E 16 " pdb=" N VAL E 17 " pdb=" CA VAL E 17 " ideal model delta harmonic sigma weight residual -180.00 -166.78 -13.22 0 5.00e+00 4.00e-02 6.99e+00 dihedral pdb=" CA LEU F 16 " pdb=" C LEU F 16 " pdb=" N VAL F 17 " pdb=" CA VAL F 17 " ideal model delta harmonic sigma weight residual -180.00 -166.79 -13.21 0 5.00e+00 4.00e-02 6.99e+00 dihedral pdb=" CA LEU A 16 " pdb=" C LEU A 16 " pdb=" N VAL A 17 " pdb=" CA VAL A 17 " ideal model delta harmonic sigma weight residual 180.00 -166.79 -13.21 0 5.00e+00 4.00e-02 6.98e+00 ... (remaining 2277 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 340 0.038 - 0.076: 211 0.076 - 0.115: 52 0.115 - 0.153: 26 0.153 - 0.191: 11 Chirality restraints: 640 Sorted by residual: chirality pdb=" CG LEU P 27 " pdb=" CB LEU P 27 " pdb=" CD1 LEU P 27 " pdb=" CD2 LEU P 27 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 9.11e-01 chirality pdb=" CB VAL H 32 " pdb=" CA VAL H 32 " pdb=" CG1 VAL H 32 " pdb=" CG2 VAL H 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.71e-01 chirality pdb=" CB VAL L 32 " pdb=" CA VAL L 32 " pdb=" CG1 VAL L 32 " pdb=" CG2 VAL L 32 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.57e-01 ... (remaining 637 not shown) Planarity restraints: 720 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR P 37 " 0.009 2.00e-02 2.50e+03 8.17e-03 1.34e+00 pdb=" CG TYR P 37 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR P 37 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR P 37 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR P 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR P 37 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR P 37 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR P 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR K 37 " 0.007 2.00e-02 2.50e+03 6.15e-03 7.55e-01 pdb=" CG TYR K 37 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR K 37 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR K 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR K 37 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR K 37 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR K 37 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR K 37 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 37 " 0.007 2.00e-02 2.50e+03 6.12e-03 7.50e-01 pdb=" CG TYR C 37 " -0.015 2.00e-02 2.50e+03 pdb=" CD1 TYR C 37 " 0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR C 37 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR C 37 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR C 37 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR C 37 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR C 37 " -0.001 2.00e-02 2.50e+03 ... (remaining 717 not shown) Histogram of nonbonded interaction distances: 2.48 - 2.97: 1920 2.97 - 3.45: 3559 3.45 - 3.93: 7153 3.93 - 4.42: 7709 4.42 - 4.90: 13622 Nonbonded interactions: 33963 Sorted by model distance: nonbonded pdb=" OG1 THR I 36 " pdb=" O HOH I 101 " model vdw 2.485 3.040 nonbonded pdb=" OG1 THR J 36 " pdb=" O HOH J 101 " model vdw 2.488 3.040 nonbonded pdb=" OG1 THR M 36 " pdb=" O HOH M 101 " model vdw 2.521 3.040 nonbonded pdb=" OG1 THR R 36 " pdb=" O HOH R 101 " model vdw 2.525 3.040 nonbonded pdb=" OG1 THR E 36 " pdb=" O HOH E 101 " model vdw 2.539 3.040 ... (remaining 33958 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain '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' } 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: 1.750 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.420 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:5.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.190 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8579 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 : 0.009 0.106 4100 Z= 0.763 Angle : 0.664 5.048 5520 Z= 0.381 Chirality : 0.055 0.191 640 Planarity : 0.002 0.008 720 Dihedral : 11.454 44.371 1320 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % 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 aren not related in a simple way. whole: -2.90 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG M 11 TYR 0.020 0.003 TYR P 37 PHE 0.009 0.002 PHE M 15 HIS 0.007 0.003 HIS F 18 Details of bonding type rmsd covalent geometry : bond 0.00531 ( 4080) covalent geometry : angle 0.66414 ( 5520) hydrogen bonds : bond 0.17944 ( 115) hydrogen bonds : angle 7.21136 ( 342) Misc. bond : bond 0.10413 ( 20) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.097 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.0750 time to fit residues: 5.5821 Evaluate side-chains 39 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 9.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 37 optimal weight: 6.9990 overall best weight: 5.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 ASN B 35 ASN C 35 ASN D 35 ASN E 14 ASN E 22 ASN E 35 ASN F 22 ASN F 35 ASN G 35 ASN H 35 ASN ** I 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** I 22 ASN I 35 ASN J 14 ASN J 22 ASN J 35 ASN K 35 ASN L 35 ASN M 14 ASN M 22 ASN M 35 ASN N 22 ASN N 35 ASN P 35 ASN Q 14 ASN Q 22 ASN Q 35 ASN R 22 ASN R 35 ASN Total number of N/Q/H flips: 29 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4166 r_free = 0.4166 target = 0.144567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.083962 restraints weight = 4086.230| |-----------------------------------------------------------------------------| r_work (start): 0.3347 rms_B_bonded: 2.48 r_work: 0.3209 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 3.95 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4100 Z= 0.241 Angle : 0.610 4.774 5520 Z= 0.349 Chirality : 0.052 0.164 640 Planarity : 0.003 0.010 720 Dihedral : 5.612 13.983 560 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.23 % Allowed : 5.91 % Favored : 93.86 % 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 aren not related in a simple way. whole: -2.81 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.13 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG J 11 TYR 0.011 0.002 TYR C 37 PHE 0.013 0.002 PHE Q 23 HIS 0.008 0.002 HIS Q 18 Details of bonding type rmsd covalent geometry : bond 0.00529 ( 4080) covalent geometry : angle 0.61042 ( 5520) hydrogen bonds : bond 0.03953 ( 115) hydrogen bonds : angle 5.28256 ( 342) Misc. bond : bond 0.00188 ( 20) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 47 time to evaluate : 0.101 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 47 average time/residue: 0.0911 time to fit residues: 5.0737 Evaluate side-chains 34 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 34 time to evaluate : 0.160 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 30.0000 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 26 optimal weight: 10.0000 chunk 14 optimal weight: 8.9990 chunk 18 optimal weight: 9.9990 chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 14 ASN D 35 ASN G 35 ASN I 14 ASN K 31 ASN P 35 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.144168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.083317 restraints weight = 4107.944| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.47 r_work: 0.3193 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8846 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 4100 Z= 0.299 Angle : 0.628 5.326 5520 Z= 0.357 Chirality : 0.053 0.174 640 Planarity : 0.003 0.012 720 Dihedral : 5.852 15.067 560 Min Nonbonded Distance : 2.665 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.80 % Favored : 97.20 % Rotamer: Outliers : 0.23 % Allowed : 7.05 % Favored : 92.73 % 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 aren not related in a simple way. whole: -2.91 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 11 TYR 0.010 0.002 TYR D 37 PHE 0.013 0.002 PHE J 23 HIS 0.009 0.003 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00651 ( 4080) covalent geometry : angle 0.62773 ( 5520) hydrogen bonds : bond 0.04210 ( 115) hydrogen bonds : angle 5.07458 ( 342) Misc. bond : bond 0.00241 ( 20) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.105 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 39 average time/residue: 0.1001 time to fit residues: 4.6653 Evaluate side-chains 28 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 28 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 chunk 38 optimal weight: 10.0000 chunk 8 optimal weight: 5.9990 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 30.0000 chunk 33 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 15 optimal weight: 6.9990 chunk 5 optimal weight: 10.0000 overall best weight: 4.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 ASN D 35 ASN G 35 ASN K 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.145533 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.084001 restraints weight = 4578.654| |-----------------------------------------------------------------------------| r_work (start): 0.3342 rms_B_bonded: 2.58 r_work: 0.3204 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 4100 Z= 0.235 Angle : 0.579 4.797 5520 Z= 0.327 Chirality : 0.050 0.200 640 Planarity : 0.002 0.008 720 Dihedral : 5.767 15.773 560 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.23 % Allowed : 6.82 % Favored : 92.95 % 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 aren not related in a simple way. whole: -2.92 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.22 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 11 TYR 0.018 0.002 TYR E 37 PHE 0.011 0.002 PHE L 23 HIS 0.007 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00511 ( 4080) covalent geometry : angle 0.57885 ( 5520) hydrogen bonds : bond 0.03649 ( 115) hydrogen bonds : angle 4.87106 ( 342) Misc. bond : bond 0.00175 ( 20) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.129 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 35 average time/residue: 0.0902 time to fit residues: 3.8170 Evaluate side-chains 29 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 28 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 7 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 10.0000 chunk 21 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 39 optimal weight: 4.9990 chunk 6 optimal weight: 20.0000 chunk 3 optimal weight: 0.1980 chunk 12 optimal weight: 20.0000 overall best weight: 4.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN F 14 ASN G 35 ASN P 35 ASN R 14 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4169 r_free = 0.4169 target = 0.145810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.084296 restraints weight = 4552.490| |-----------------------------------------------------------------------------| r_work (start): 0.3345 rms_B_bonded: 2.58 r_work: 0.3207 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3098 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8841 moved from start: 0.2537 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 4100 Z= 0.219 Angle : 0.566 4.665 5520 Z= 0.319 Chirality : 0.049 0.230 640 Planarity : 0.002 0.007 720 Dihedral : 5.737 16.116 560 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.23 % Allowed : 7.50 % Favored : 92.27 % 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 aren not related in a simple way. whole: -2.88 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.19 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG R 11 TYR 0.013 0.002 TYR N 37 PHE 0.015 0.002 PHE P 23 HIS 0.007 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 4080) covalent geometry : angle 0.56577 ( 5520) hydrogen bonds : bond 0.03478 ( 115) hydrogen bonds : angle 4.79462 ( 342) Misc. bond : bond 0.00162 ( 20) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.201 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.1094 time to fit residues: 5.2438 Evaluate side-chains 31 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 38 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 chunk 2 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 23 optimal weight: 10.0000 chunk 26 optimal weight: 10.0000 chunk 7 optimal weight: 6.9990 chunk 37 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 chunk 20 optimal weight: 20.0000 overall best weight: 7.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN ** F 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 35 ASN K 35 ASN N 14 ASN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4149 r_free = 0.4149 target = 0.144438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.082910 restraints weight = 4706.020| |-----------------------------------------------------------------------------| r_work (start): 0.3320 rms_B_bonded: 2.59 r_work: 0.3178 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3069 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3069 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2673 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 4100 Z= 0.335 Angle : 0.652 5.361 5520 Z= 0.368 Chirality : 0.055 0.259 640 Planarity : 0.003 0.009 720 Dihedral : 5.975 16.946 560 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 0.23 % Allowed : 8.18 % Favored : 91.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.93 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.23 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG S 11 TYR 0.020 0.002 TYR E 37 PHE 0.013 0.002 PHE Q 23 HIS 0.009 0.003 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00726 ( 4080) covalent geometry : angle 0.65214 ( 5520) hydrogen bonds : bond 0.04362 ( 115) hydrogen bonds : angle 4.98730 ( 342) Misc. bond : bond 0.00246 ( 20) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.201 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.0853 time to fit residues: 4.0399 Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 29 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 0.8980 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 10.0000 chunk 22 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 1 optimal weight: 0.3980 chunk 8 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 overall best weight: 3.4586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 35 ASN P 35 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.146851 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.085561 restraints weight = 4557.604| |-----------------------------------------------------------------------------| r_work (start): 0.3360 rms_B_bonded: 2.56 r_work: 0.3220 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3111 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3111 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8821 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4100 Z= 0.167 Angle : 0.542 5.649 5520 Z= 0.301 Chirality : 0.047 0.233 640 Planarity : 0.002 0.007 720 Dihedral : 5.627 16.157 560 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 0.23 % Allowed : 8.41 % Favored : 91.36 % 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 aren not related in a simple way. whole: -2.91 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 11 TYR 0.014 0.002 TYR N 37 PHE 0.013 0.001 PHE G 23 HIS 0.005 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00363 ( 4080) covalent geometry : angle 0.54226 ( 5520) hydrogen bonds : bond 0.03043 ( 115) hydrogen bonds : angle 4.64702 ( 342) Misc. bond : bond 0.00123 ( 20) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 38 time to evaluate : 0.105 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.0871 time to fit residues: 4.0670 Evaluate side-chains 33 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.147 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 9.9990 chunk 35 optimal weight: 5.9990 chunk 16 optimal weight: 20.0000 chunk 11 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 4.9990 overall best weight: 3.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 35 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4176 r_free = 0.4176 target = 0.146797 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.085342 restraints weight = 4609.531| |-----------------------------------------------------------------------------| r_work (start): 0.3364 rms_B_bonded: 2.59 r_work: 0.3220 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3110 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 4100 Z= 0.170 Angle : 0.543 5.621 5520 Z= 0.302 Chirality : 0.048 0.235 640 Planarity : 0.002 0.009 720 Dihedral : 5.598 16.140 560 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.23 % Allowed : 8.64 % Favored : 91.14 % 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 aren not related in a simple way. whole: -2.89 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.20 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 11 TYR 0.014 0.002 TYR R 37 PHE 0.015 0.001 PHE S 23 HIS 0.005 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 4080) covalent geometry : angle 0.54265 ( 5520) hydrogen bonds : bond 0.03089 ( 115) hydrogen bonds : angle 4.60522 ( 342) Misc. bond : bond 0.00125 ( 20) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.158 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.1042 time to fit residues: 4.6443 Evaluate side-chains 33 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 32 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 2 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 4 optimal weight: 30.0000 chunk 28 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 17 optimal weight: 6.9990 chunk 3 optimal weight: 6.9990 chunk 36 optimal weight: 6.9990 chunk 37 optimal weight: 4.9990 chunk 8 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 35 ASN P 35 ASN ** S 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.144708 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.082736 restraints weight = 4981.022| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 2.67 r_work: 0.3176 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3066 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3066 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8860 moved from start: 0.2684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 4100 Z= 0.319 Angle : 0.649 5.257 5520 Z= 0.363 Chirality : 0.054 0.278 640 Planarity : 0.003 0.009 720 Dihedral : 5.949 17.065 560 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer: Outliers : 0.68 % Allowed : 9.32 % Favored : 90.00 % 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 aren not related in a simple way. whole: -2.99 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.27 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG H 11 TYR 0.020 0.002 TYR E 37 PHE 0.013 0.002 PHE Q 23 HIS 0.008 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00692 ( 4080) covalent geometry : angle 0.64875 ( 5520) hydrogen bonds : bond 0.04201 ( 115) hydrogen bonds : angle 4.88605 ( 342) Misc. bond : bond 0.00225 ( 20) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 34 time to evaluate : 0.109 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 36 average time/residue: 0.0836 time to fit residues: 3.5872 Evaluate side-chains 31 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 30 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 10.0000 chunk 28 optimal weight: 20.0000 chunk 29 optimal weight: 5.9990 chunk 4 optimal weight: 20.0000 chunk 37 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 13 optimal weight: 9.9990 chunk 6 optimal weight: 20.0000 chunk 9 optimal weight: 2.9990 chunk 22 optimal weight: 20.0000 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 35 ASN K 35 ASN ** T 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.146387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.084468 restraints weight = 4834.960| |-----------------------------------------------------------------------------| r_work (start): 0.3344 rms_B_bonded: 2.64 r_work: 0.3202 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.3093 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3093 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 4100 Z= 0.191 Angle : 0.565 6.192 5520 Z= 0.312 Chirality : 0.049 0.256 640 Planarity : 0.002 0.009 720 Dihedral : 5.665 16.527 560 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.23 % Allowed : 10.45 % Favored : 89.32 % 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 aren not related in a simple way. whole: -2.96 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.25 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG T 11 TYR 0.016 0.002 TYR R 37 PHE 0.013 0.002 PHE O 23 HIS 0.006 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 4080) covalent geometry : angle 0.56500 ( 5520) hydrogen bonds : bond 0.03263 ( 115) hydrogen bonds : angle 4.68268 ( 342) Misc. bond : bond 0.00138 ( 20) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1000 Ramachandran restraints generated. 500 Oldfield, 0 Emsley, 500 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.156 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.0983 time to fit residues: 4.3754 Evaluate side-chains 36 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 36 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 27 optimal weight: 2.9990 chunk 3 optimal weight: 10.0000 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 10.0000 chunk 29 optimal weight: 8.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 17 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 36 optimal weight: 20.0000 overall best weight: 2.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN G 35 ASN K 35 ASN P 35 ASN ** T 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4181 r_free = 0.4181 target = 0.147445 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086146 restraints weight = 4403.376| |-----------------------------------------------------------------------------| r_work (start): 0.3374 rms_B_bonded: 2.56 r_work: 0.3230 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8830 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 4100 Z= 0.145 Angle : 0.532 6.088 5520 Z= 0.293 Chirality : 0.047 0.230 640 Planarity : 0.002 0.009 720 Dihedral : 5.500 15.911 560 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.23 % Allowed : 10.23 % Favored : 89.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: -2.91 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.21 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG S 11 TYR 0.014 0.002 TYR N 37 PHE 0.014 0.001 PHE G 23 HIS 0.005 0.002 HIS J 18 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 4080) covalent geometry : angle 0.53163 ( 5520) hydrogen bonds : bond 0.02789 ( 115) hydrogen bonds : angle 4.53646 ( 342) Misc. bond : bond 0.00102 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1477.33 seconds wall clock time: 25 minutes 59.24 seconds (1559.24 seconds total)