Starting phenix.real_space_refine on Wed Jul 23 18:58:09 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8az5_15754/07_2025/8az5_15754.cif Found real_map, /net/cci-nas-00/data/ceres_data/8az5_15754/07_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_15754/07_2025/8az5_15754.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8az5_15754/07_2025/8az5_15754.map" model { file = "/net/cci-nas-00/data/ceres_data/8az5_15754/07_2025/8az5_15754.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8az5_15754/07_2025/8az5_15754.cif" } resolution = 2.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/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: 3.53, per 1000 atoms: 0.87 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: 1.35 Conformation dependent library (CDL) restraints added in 478.1 milliseconds 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: 0.76 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: 1.10 Time building geometry restraints manager: 1.54 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: 2.170 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.600 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:14.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.060 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.007 0.003 HIS F 18 PHE 0.009 0.002 PHE M 15 TYR 0.020 0.003 TYR P 37 ARG 0.002 0.001 ARG M 11 Details of bonding type rmsd hydrogen bonds : bond 0.17944 ( 115) hydrogen bonds : angle 7.21136 ( 342) covalent geometry : bond 0.00531 ( 4080) covalent geometry : angle 0.66414 ( 5520) 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 : 0.490 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 61 average time/residue: 0.1902 time to fit residues: 14.3278 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 : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 31 optimal weight: 6.9990 chunk 12 optimal weight: 7.9990 chunk 19 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 36 optimal weight: 20.0000 chunk 11 optimal weight: 0.9980 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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 31 ASN D 35 ASN E 22 ASN E 35 ASN F 22 ASN F 35 ASN G 31 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 31 ASN K 35 ASN L 35 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: 30 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4207 r_free = 0.4207 target = 0.147682 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3411 r_free = 0.3411 target = 0.087006 restraints weight = 4005.076| |-----------------------------------------------------------------------------| r_work (start): 0.3401 rms_B_bonded: 2.45 r_work: 0.3265 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8806 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 4100 Z= 0.122 Angle : 0.514 3.743 5520 Z= 0.293 Chirality : 0.047 0.135 640 Planarity : 0.002 0.010 720 Dihedral : 5.224 13.805 560 Min Nonbonded Distance : 2.682 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 5.91 % Favored : 94.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.09 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.010 0.001 PHE O 23 TYR 0.009 0.001 TYR R 37 ARG 0.001 0.000 ARG J 11 Details of bonding type rmsd hydrogen bonds : bond 0.02765 ( 115) hydrogen bonds : angle 5.09795 ( 342) covalent geometry : bond 0.00259 ( 4080) covalent geometry : angle 0.51358 ( 5520) Misc. bond : bond 0.00086 ( 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 43 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.526 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 43 average time/residue: 0.2228 time to fit residues: 11.6310 Evaluate side-chains 30 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 30 time to evaluate : 0.474 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 9.9990 chunk 20 optimal weight: 30.0000 chunk 10 optimal weight: 9.9990 chunk 4 optimal weight: 30.0000 chunk 22 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 13 optimal weight: 9.9990 chunk 16 optimal weight: 8.9990 chunk 19 optimal weight: 0.2980 chunk 12 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 overall best weight: 7.2588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 35 ASN E 14 ASN G 35 ASN I 14 ASN L 35 ASN M 14 ASN P 35 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4152 r_free = 0.4152 target = 0.143683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3335 r_free = 0.3335 target = 0.082719 restraints weight = 4203.979| |-----------------------------------------------------------------------------| r_work (start): 0.3328 rms_B_bonded: 2.50 r_work: 0.3187 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3077 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3077 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8848 moved from start: 0.2359 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.043 4100 Z= 0.338 Angle : 0.658 5.554 5520 Z= 0.377 Chirality : 0.056 0.188 640 Planarity : 0.003 0.013 720 Dihedral : 5.910 14.996 560 Min Nonbonded Distance : 2.668 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.23 % Allowed : 6.14 % Favored : 93.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.24), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.003 HIS J 18 PHE 0.013 0.002 PHE Q 23 TYR 0.009 0.002 TYR D 37 ARG 0.001 0.000 ARG R 11 Details of bonding type rmsd hydrogen bonds : bond 0.04413 ( 115) hydrogen bonds : angle 5.13748 ( 342) covalent geometry : bond 0.00738 ( 4080) covalent geometry : angle 0.65801 ( 5520) Misc. bond : bond 0.00256 ( 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 42 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 41 time to evaluate : 0.447 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.2286 time to fit residues: 11.7034 Evaluate side-chains 31 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 31 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 3.9990 chunk 18 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 3 optimal weight: 4.9990 chunk 2 optimal weight: 10.0000 chunk 32 optimal weight: 9.9990 chunk 4 optimal weight: 20.0000 chunk 6 optimal weight: 20.0000 chunk 26 optimal weight: 9.9990 chunk 22 optimal weight: 20.0000 overall best weight: 5.9988 ------------------------------------------------------------------------------- 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 31 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 = 0.4158 r_free = 0.4158 target = 0.144701 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3348 r_free = 0.3348 target = 0.083397 restraints weight = 4435.920| |-----------------------------------------------------------------------------| r_work (start): 0.3334 rms_B_bonded: 2.54 r_work: 0.3192 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3083 rms_B_bonded: 4.08 restraints_weight: 0.2500 r_work (final): 0.3083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 4100 Z= 0.282 Angle : 0.610 5.094 5520 Z= 0.346 Chirality : 0.052 0.209 640 Planarity : 0.003 0.008 720 Dihedral : 5.868 15.863 560 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.23 % Allowed : 7.27 % Favored : 92.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.008 0.003 HIS J 18 PHE 0.012 0.002 PHE Q 23 TYR 0.017 0.002 TYR E 37 ARG 0.001 0.000 ARG S 11 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 115) hydrogen bonds : angle 4.95788 ( 342) covalent geometry : bond 0.00613 ( 4080) covalent geometry : angle 0.61038 ( 5520) Misc. bond : bond 0.00210 ( 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 37 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 36 time to evaluate : 0.441 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.2839 time to fit residues: 12.7122 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 : 0.475 ------------------------------------------------------------------------------- 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 35 optimal weight: 3.9990 chunk 28 optimal weight: 20.0000 chunk 24 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 31 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 2 optimal weight: 10.0000 chunk 3 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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 P 35 ASN R 14 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 = 0.146521 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.085075 restraints weight = 4572.500| |-----------------------------------------------------------------------------| r_work (start): 0.3357 rms_B_bonded: 2.57 r_work: 0.3219 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2547 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4100 Z= 0.182 Angle : 0.539 4.435 5520 Z= 0.303 Chirality : 0.047 0.203 640 Planarity : 0.002 0.006 720 Dihedral : 5.609 15.866 560 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 0.23 % Allowed : 7.73 % Favored : 92.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS J 18 PHE 0.013 0.001 PHE P 23 TYR 0.014 0.002 TYR E 37 ARG 0.001 0.000 ARG S 11 Details of bonding type rmsd hydrogen bonds : bond 0.03172 ( 115) hydrogen bonds : angle 4.71377 ( 342) covalent geometry : bond 0.00396 ( 4080) covalent geometry : angle 0.53880 ( 5520) Misc. bond : bond 0.00135 ( 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 : 0.469 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.2341 time to fit residues: 11.4101 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 : 0.472 ------------------------------------------------------------------------------- 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 13 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 chunk 36 optimal weight: 7.9990 chunk 3 optimal weight: 7.9990 chunk 33 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 22 optimal weight: 20.0000 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 overall best weight: 2.7990 ------------------------------------------------------------------------------- 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 ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4186 r_free = 0.4186 target = 0.147414 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3388 r_free = 0.3388 target = 0.086066 restraints weight = 4427.646| |-----------------------------------------------------------------------------| r_work (start): 0.3377 rms_B_bonded: 2.56 r_work: 0.3235 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3124 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8826 moved from start: 0.2621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 4100 Z= 0.138 Angle : 0.509 5.531 5520 Z= 0.284 Chirality : 0.046 0.204 640 Planarity : 0.002 0.007 720 Dihedral : 5.472 15.568 560 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % Rotamer: Outliers : 0.23 % Allowed : 7.95 % Favored : 91.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.84 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS J 18 PHE 0.012 0.001 PHE L 23 TYR 0.014 0.001 TYR R 37 ARG 0.000 0.000 ARG S 11 Details of bonding type rmsd hydrogen bonds : bond 0.02717 ( 115) hydrogen bonds : angle 4.57740 ( 342) covalent geometry : bond 0.00298 ( 4080) covalent geometry : angle 0.50881 ( 5520) Misc. bond : bond 0.00099 ( 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 : 0.500 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.2230 time to fit residues: 10.6010 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 : 0.432 ------------------------------------------------------------------------------- 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 0 optimal weight: 10.0000 chunk 9 optimal weight: 8.9990 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 20.0000 chunk 37 optimal weight: 0.8980 chunk 32 optimal weight: 9.9990 chunk 38 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 4 optimal weight: 30.0000 chunk 24 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 overall best weight: 6.5788 ------------------------------------------------------------------------------- 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 N 14 ASN P 35 ASN ** R 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** T 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4150 r_free = 0.4150 target = 0.144683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.083419 restraints weight = 4421.236| |-----------------------------------------------------------------------------| r_work (start): 0.3326 rms_B_bonded: 2.54 r_work: 0.3187 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3078 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8853 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.037 4100 Z= 0.307 Angle : 0.626 5.012 5520 Z= 0.354 Chirality : 0.053 0.263 640 Planarity : 0.003 0.009 720 Dihedral : 5.897 16.688 560 Min Nonbonded Distance : 2.635 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.008 0.002 HIS J 18 PHE 0.012 0.002 PHE Q 23 TYR 0.020 0.002 TYR E 37 ARG 0.001 0.000 ARG S 11 Details of bonding type rmsd hydrogen bonds : bond 0.04118 ( 115) hydrogen bonds : angle 4.87203 ( 342) covalent geometry : bond 0.00665 ( 4080) covalent geometry : angle 0.62629 ( 5520) Misc. bond : bond 0.00222 ( 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 36 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.442 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.2222 time to fit residues: 9.8916 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 : 0.540 ------------------------------------------------------------------------------- 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 4 optimal weight: 20.0000 chunk 26 optimal weight: 5.9990 chunk 14 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 38 optimal weight: 9.9990 chunk 39 optimal weight: 4.9990 chunk 36 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 21 optimal weight: 9.9990 chunk 5 optimal weight: 9.9990 chunk 10 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: 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 = 0.4164 r_free = 0.4164 target = 0.145893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.084439 restraints weight = 4618.628| |-----------------------------------------------------------------------------| r_work (start): 0.3348 rms_B_bonded: 2.59 r_work: 0.3203 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3095 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3095 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8845 moved from start: 0.2713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 4100 Z= 0.234 Angle : 0.570 5.436 5520 Z= 0.323 Chirality : 0.049 0.253 640 Planarity : 0.002 0.007 720 Dihedral : 5.739 16.619 560 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 3.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.60 % Favored : 97.40 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 18 PHE 0.013 0.002 PHE O 23 TYR 0.015 0.002 TYR E 37 ARG 0.001 0.000 ARG S 11 Details of bonding type rmsd hydrogen bonds : bond 0.03580 ( 115) hydrogen bonds : angle 4.77186 ( 342) covalent geometry : bond 0.00506 ( 4080) covalent geometry : angle 0.57004 ( 5520) Misc. bond : bond 0.00171 ( 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 40 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 39 time to evaluate : 0.485 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 40 average time/residue: 0.2339 time to fit residues: 11.4148 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 : 0.442 ------------------------------------------------------------------------------- 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 30 optimal weight: 20.0000 chunk 36 optimal weight: 5.9990 chunk 37 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 4 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 chunk 31 optimal weight: 5.9990 chunk 6 optimal weight: 5.9990 chunk 35 optimal weight: 5.9990 overall best weight: 3.8188 ------------------------------------------------------------------------------- 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 = 0.4169 r_free = 0.4169 target = 0.146485 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.085358 restraints weight = 4359.454| |-----------------------------------------------------------------------------| r_work (start): 0.3361 rms_B_bonded: 2.54 r_work: 0.3214 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3105 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3105 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8835 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 4100 Z= 0.183 Angle : 0.544 5.693 5520 Z= 0.305 Chirality : 0.047 0.250 640 Planarity : 0.002 0.009 720 Dihedral : 5.608 16.233 560 Min Nonbonded Distance : 2.648 Molprobity Statistics. All-atom Clashscore : 3.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 0.23 % Allowed : 9.32 % Favored : 90.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 HIS 0.006 0.002 HIS J 18 PHE 0.011 0.001 PHE G 23 TYR 0.016 0.002 TYR R 37 ARG 0.001 0.000 ARG R 11 Details of bonding type rmsd hydrogen bonds : bond 0.03151 ( 115) hydrogen bonds : angle 4.65631 ( 342) covalent geometry : bond 0.00396 ( 4080) covalent geometry : angle 0.54417 ( 5520) Misc. bond : bond 0.00141 ( 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 38 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.484 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 38 average time/residue: 0.2363 time to fit residues: 10.9368 Evaluate side-chains 34 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 33 time to evaluate : 0.455 ------------------------------------------------------------------------------- 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 31 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 1 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 39 optimal weight: 3.9990 chunk 20 optimal weight: 20.0000 chunk 12 optimal weight: 9.9990 chunk 3 optimal weight: 0.8980 chunk 13 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.147944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3400 r_free = 0.3400 target = 0.086694 restraints weight = 4234.665| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 2.54 r_work: 0.3245 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3135 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8822 moved from start: 0.2710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.015 4100 Z= 0.123 Angle : 0.504 5.924 5520 Z= 0.281 Chirality : 0.045 0.217 640 Planarity : 0.002 0.009 720 Dihedral : 5.394 15.599 560 Min Nonbonded Distance : 2.651 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.18 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS J 18 PHE 0.014 0.001 PHE L 23 TYR 0.012 0.002 TYR Q 37 ARG 0.000 0.000 ARG S 11 Details of bonding type rmsd hydrogen bonds : bond 0.02519 ( 115) hydrogen bonds : angle 4.50508 ( 342) covalent geometry : bond 0.00263 ( 4080) covalent geometry : angle 0.50352 ( 5520) Misc. bond : bond 0.00082 ( 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 39 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.501 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 39 average time/residue: 0.2288 time to fit residues: 10.9677 Evaluate side-chains 35 residues out of total 440 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 5.9990 chunk 27 optimal weight: 7.9990 chunk 34 optimal weight: 9.9990 chunk 2 optimal weight: 10.0000 chunk 23 optimal weight: 10.0000 chunk 13 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 14 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 10.0000 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 K 35 ASN L 35 ASN P 35 ASN ** T 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4156 r_free = 0.4156 target = 0.145330 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.084055 restraints weight = 4410.406| |-----------------------------------------------------------------------------| r_work (start): 0.3335 rms_B_bonded: 2.55 r_work: 0.3191 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3081 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8849 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 4100 Z= 0.273 Angle : 0.605 5.442 5520 Z= 0.341 Chirality : 0.051 0.263 640 Planarity : 0.002 0.009 720 Dihedral : 5.779 16.879 560 Min Nonbonded Distance : 2.649 Molprobity Statistics. All-atom Clashscore : 3.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 0.23 % Allowed : 10.00 % Favored : 89.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.95 (0.23), residues: 500 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.24 (0.18), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS J 18 PHE 0.013 0.002 PHE K 23 TYR 0.018 0.002 TYR E 37 ARG 0.001 0.000 ARG S 11 Details of bonding type rmsd hydrogen bonds : bond 0.03854 ( 115) hydrogen bonds : angle 4.76402 ( 342) covalent geometry : bond 0.00591 ( 4080) covalent geometry : angle 0.60511 ( 5520) Misc. bond : bond 0.00194 ( 20) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4344.21 seconds wall clock time: 78 minutes 26.86 seconds (4706.86 seconds total)