Starting phenix.real_space_refine on Sun Aug 24 18:39:01 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tob_41442/08_2025/8tob_41442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tob_41442/08_2025/8tob_41442.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.14 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8tob_41442/08_2025/8tob_41442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tob_41442/08_2025/8tob_41442.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8tob_41442/08_2025/8tob_41442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tob_41442/08_2025/8tob_41442.map" } resolution = 3.14 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 132 5.16 5 C 14014 2.51 5 N 3674 2.21 5 O 4422 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 74 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: 22242 Number of models: 1 Model: "" Number of chains: 44 Chain: "GA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "HA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "IA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "JA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "KA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "LA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "MA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "NA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "OA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "PA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "QA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "RA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "SA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "TA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "UA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "VA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "AA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "BA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "CA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "DA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "EA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "FA" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 70, 520 Classifications: {'peptide': 70} Link IDs: {'PTRANS': 1, 'TRANS': 68} Chain: "GB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "HB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "IB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "JB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "KB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "LB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "MB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "NB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "OB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "PB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "QB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "RB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "SB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "TB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "UB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "VB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "AB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "BB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "CB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "DB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "EB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Chain: "FB" Number of atoms: 491 Number of conformers: 1 Conformer: "" Number of residues, atoms: 69, 491 Classifications: {'peptide': 69} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 65} Time building chain proxies: 4.21, per 1000 atoms: 0.19 Number of scatterers: 22242 At special positions: 0 Unit cell: (74.048, 74.048, 307.84, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 132 16.00 O 4422 8.00 N 3674 7.00 C 14014 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=44, symmetry=0 Simple disulfide: pdb=" SG CYSGA 57 " - pdb=" SG CYSGA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSHA 57 " - pdb=" SG CYSHA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSIA 57 " - pdb=" SG CYSIA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSJA 57 " - pdb=" SG CYSJA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSKA 57 " - pdb=" SG CYSKA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSLA 57 " - pdb=" SG CYSLA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSMA 57 " - pdb=" SG CYSMA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSNA 57 " - pdb=" SG CYSNA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSOA 57 " - pdb=" SG CYSOA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSPA 57 " - pdb=" SG CYSPA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSQA 57 " - pdb=" SG CYSQA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSRA 57 " - pdb=" SG CYSRA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSSA 57 " - pdb=" SG CYSSA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSTA 57 " - pdb=" SG CYSTA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSUA 57 " - pdb=" SG CYSUA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSVA 57 " - pdb=" SG CYSVA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSAA 57 " - pdb=" SG CYSAA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSBA 57 " - pdb=" SG CYSBA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSCA 57 " - pdb=" SG CYSCA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSDA 57 " - pdb=" SG CYSDA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSEA 57 " - pdb=" SG CYSEA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSFA 57 " - pdb=" SG CYSFA 67 " distance=2.03 Simple disulfide: pdb=" SG CYSGB 132 " - pdb=" SG CYSGB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSHB 132 " - pdb=" SG CYSHB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSIB 132 " - pdb=" SG CYSIB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSJB 132 " - pdb=" SG CYSJB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSKB 132 " - pdb=" SG CYSKB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSLB 132 " - pdb=" SG CYSLB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSMB 132 " - pdb=" SG CYSMB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSNB 132 " - pdb=" SG CYSNB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSOB 132 " - pdb=" SG CYSOB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSPB 132 " - pdb=" SG CYSPB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSQB 132 " - pdb=" SG CYSQB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSRB 132 " - pdb=" SG CYSRB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSSB 132 " - pdb=" SG CYSSB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSTB 132 " - pdb=" SG CYSTB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSUB 132 " - pdb=" SG CYSUB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSVB 132 " - pdb=" SG CYSVB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSAB 132 " - pdb=" SG CYSAB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSBB 132 " - pdb=" SG CYSBB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSCB 132 " - pdb=" SG CYSCB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSDB 132 " - pdb=" SG CYSDB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSEB 132 " - pdb=" SG CYSEB 145 " distance=2.03 Simple disulfide: pdb=" SG CYSFB 132 " - pdb=" SG CYSFB 145 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.97 Conformation dependent library (CDL) restraints added in 929.4 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 5632 Finding SS restraints... Secondary structure from input PDB file: 96 helices and 22 sheets defined 39.1% alpha, 12.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'GA' and resid 9 through 25 Processing helix chain 'GA' and resid 31 through 49 Processing helix chain 'GA' and resid 50 through 61 Processing helix chain 'HA' and resid 10 through 25 Processing helix chain 'HA' and resid 31 through 50 removed outlier: 3.572A pdb=" N LEUHA 50 " --> pdb=" O GLUHA 46 " (cutoff:3.500A) Processing helix chain 'HA' and resid 50 through 61 Processing helix chain 'IA' and resid 10 through 25 Processing helix chain 'IA' and resid 31 through 49 Processing helix chain 'IA' and resid 50 through 61 Processing helix chain 'JA' and resid 10 through 25 Processing helix chain 'JA' and resid 31 through 49 removed outlier: 3.528A pdb=" N ILEJA 35 " --> pdb=" O TYRJA 31 " (cutoff:3.500A) Processing helix chain 'JA' and resid 50 through 61 Processing helix chain 'KA' and resid 10 through 25 Processing helix chain 'KA' and resid 31 through 49 Processing helix chain 'KA' and resid 50 through 60 Processing helix chain 'LA' and resid 10 through 25 Processing helix chain 'LA' and resid 31 through 59 removed outlier: 3.578A pdb=" N LYSLA 37 " --> pdb=" O ASNLA 33 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N GLYLA 48 " --> pdb=" O METLA 44 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEULA 50 " --> pdb=" O GLULA 46 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYSLA 51 " --> pdb=" O THRLA 47 " (cutoff:3.500A) removed outlier: 4.298A pdb=" N THRLA 52 " --> pdb=" O GLYLA 48 " (cutoff:3.500A) removed outlier: 4.487A pdb=" N VALLA 53 " --> pdb=" O SERLA 49 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N THRLA 56 " --> pdb=" O THRLA 52 " (cutoff:3.500A) Processing helix chain 'MA' and resid 10 through 25 Processing helix chain 'MA' and resid 31 through 49 Processing helix chain 'MA' and resid 50 through 61 Processing helix chain 'NA' and resid 10 through 25 Processing helix chain 'NA' and resid 31 through 59 removed outlier: 3.544A pdb=" N LYSNA 37 " --> pdb=" O ASNNA 33 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N GLYNA 48 " --> pdb=" O METNA 44 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEUNA 50 " --> pdb=" O GLUNA 46 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYSNA 51 " --> pdb=" O THRNA 47 " (cutoff:3.500A) removed outlier: 4.237A pdb=" N THRNA 52 " --> pdb=" O GLYNA 48 " (cutoff:3.500A) removed outlier: 4.457A pdb=" N VALNA 53 " --> pdb=" O SERNA 49 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N THRNA 56 " --> pdb=" O THRNA 52 " (cutoff:3.500A) Processing helix chain 'OA' and resid 10 through 25 Processing helix chain 'OA' and resid 31 through 49 Processing helix chain 'OA' and resid 50 through 60 Processing helix chain 'PA' and resid 10 through 25 removed outlier: 3.629A pdb=" N METPA 14 " --> pdb=" O LEUPA 10 " (cutoff:3.500A) Processing helix chain 'PA' and resid 31 through 49 Processing helix chain 'PA' and resid 50 through 61 Processing helix chain 'QA' and resid 10 through 25 Processing helix chain 'QA' and resid 31 through 49 Processing helix chain 'QA' and resid 50 through 61 Processing helix chain 'RA' and resid 10 through 25 Processing helix chain 'RA' and resid 31 through 59 removed outlier: 3.540A pdb=" N LYSRA 37 " --> pdb=" O ASNRA 33 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEURA 50 " --> pdb=" O GLURA 46 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N LYSRA 51 " --> pdb=" O THRRA 47 " (cutoff:3.500A) removed outlier: 4.320A pdb=" N THRRA 52 " --> pdb=" O GLYRA 48 " (cutoff:3.500A) removed outlier: 4.631A pdb=" N VALRA 53 " --> pdb=" O SERRA 49 " (cutoff:3.500A) Processing helix chain 'SA' and resid 10 through 25 Processing helix chain 'SA' and resid 31 through 49 removed outlier: 3.562A pdb=" N ILESA 35 " --> pdb=" O TYRSA 31 " (cutoff:3.500A) Processing helix chain 'SA' and resid 50 through 61 Processing helix chain 'TA' and resid 10 through 25 Processing helix chain 'TA' and resid 31 through 49 Processing helix chain 'TA' and resid 50 through 61 Processing helix chain 'UA' and resid 10 through 25 Processing helix chain 'UA' and resid 31 through 49 Processing helix chain 'UA' and resid 50 through 61 Processing helix chain 'UA' and resid 74 through 78 removed outlier: 3.813A pdb=" N GLYUA 78 " --> pdb=" O ASNUA 75 " (cutoff:3.500A) Processing helix chain 'VA' and resid 10 through 25 Processing helix chain 'VA' and resid 31 through 49 Processing helix chain 'VA' and resid 50 through 61 Processing helix chain 'AA' and resid 10 through 25 Processing helix chain 'AA' and resid 31 through 50 removed outlier: 3.890A pdb=" N LEUAA 50 " --> pdb=" O GLUAA 46 " (cutoff:3.500A) Processing helix chain 'AA' and resid 50 through 61 Processing helix chain 'BA' and resid 10 through 25 Processing helix chain 'BA' and resid 31 through 49 Processing helix chain 'BA' and resid 50 through 61 Processing helix chain 'CA' and resid 10 through 25 Processing helix chain 'CA' and resid 31 through 49 Processing helix chain 'CA' and resid 50 through 61 Processing helix chain 'DA' and resid 10 through 25 Processing helix chain 'DA' and resid 31 through 49 removed outlier: 3.509A pdb=" N ILEDA 35 " --> pdb=" O TYRDA 31 " (cutoff:3.500A) Processing helix chain 'DA' and resid 50 through 61 Processing helix chain 'EA' and resid 10 through 25 Processing helix chain 'EA' and resid 31 through 59 removed outlier: 3.676A pdb=" N LYSEA 37 " --> pdb=" O ASNEA 33 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N LEUEA 50 " --> pdb=" O GLUEA 46 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N LYSEA 51 " --> pdb=" O THREA 47 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N THREA 52 " --> pdb=" O GLYEA 48 " (cutoff:3.500A) removed outlier: 4.412A pdb=" N VALEA 53 " --> pdb=" O SEREA 49 " (cutoff:3.500A) removed outlier: 3.513A pdb=" N THREA 56 " --> pdb=" O THREA 52 " (cutoff:3.500A) Processing helix chain 'FA' and resid 10 through 25 Processing helix chain 'FA' and resid 31 through 49 Processing helix chain 'FA' and resid 50 through 61 Processing helix chain 'GB' and resid 112 through 116 Processing helix chain 'GB' and resid 137 through 141 Processing helix chain 'GB' and resid 142 through 146 removed outlier: 4.133A pdb=" N ALAGB 146 " --> pdb=" O ALAGB 143 " (cutoff:3.500A) Processing helix chain 'HB' and resid 137 through 141 Processing helix chain 'HB' and resid 142 through 146 removed outlier: 3.852A pdb=" N ALAHB 146 " --> pdb=" O ALAHB 143 " (cutoff:3.500A) Processing helix chain 'IB' and resid 137 through 141 Processing helix chain 'IB' and resid 142 through 146 removed outlier: 3.858A pdb=" N ALAIB 146 " --> pdb=" O ALAIB 143 " (cutoff:3.500A) Processing helix chain 'JB' and resid 137 through 141 Processing helix chain 'KB' and resid 137 through 141 Processing helix chain 'KB' and resid 142 through 146 removed outlier: 4.164A pdb=" N ALAKB 146 " --> pdb=" O ALAKB 143 " (cutoff:3.500A) Processing helix chain 'LB' and resid 137 through 141 Processing helix chain 'LB' and resid 142 through 146 removed outlier: 4.039A pdb=" N ALALB 146 " --> pdb=" O ALALB 143 " (cutoff:3.500A) Processing helix chain 'MB' and resid 137 through 141 Processing helix chain 'NB' and resid 137 through 141 Processing helix chain 'OB' and resid 137 through 141 Processing helix chain 'PB' and resid 137 through 141 Processing helix chain 'PB' and resid 142 through 146 removed outlier: 4.061A pdb=" N ALAPB 146 " --> pdb=" O ALAPB 143 " (cutoff:3.500A) Processing helix chain 'QB' and resid 137 through 141 Processing helix chain 'RB' and resid 137 through 141 Processing helix chain 'SB' and resid 142 through 146 removed outlier: 4.003A pdb=" N ALASB 146 " --> pdb=" O ALASB 143 " (cutoff:3.500A) Processing helix chain 'TB' and resid 137 through 141 Processing helix chain 'TB' and resid 142 through 146 removed outlier: 3.694A pdb=" N ALATB 146 " --> pdb=" O ALATB 143 " (cutoff:3.500A) Processing helix chain 'UB' and resid 137 through 141 Processing helix chain 'UB' and resid 142 through 146 removed outlier: 4.093A pdb=" N ALAUB 146 " --> pdb=" O ALAUB 143 " (cutoff:3.500A) Processing helix chain 'VB' and resid 137 through 141 Processing helix chain 'AB' and resid 137 through 141 Processing helix chain 'AB' and resid 142 through 146 removed outlier: 3.782A pdb=" N ALAAB 146 " --> pdb=" O ALAAB 143 " (cutoff:3.500A) Processing helix chain 'BB' and resid 137 through 141 Processing helix chain 'BB' and resid 142 through 146 removed outlier: 4.146A pdb=" N ALABB 146 " --> pdb=" O ALABB 143 " (cutoff:3.500A) Processing helix chain 'CB' and resid 137 through 141 Processing helix chain 'DB' and resid 137 through 141 Processing helix chain 'EB' and resid 142 through 146 removed outlier: 3.711A pdb=" N ALAEB 146 " --> pdb=" O ALAEB 143 " (cutoff:3.500A) Processing helix chain 'FB' and resid 142 through 146 removed outlier: 3.983A pdb=" N ALAFB 146 " --> pdb=" O ALAFB 143 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'GB' and resid 89 through 92 Processing sheet with id=AA2, first strand: chain 'HB' and resid 89 through 92 Processing sheet with id=AA3, first strand: chain 'IB' and resid 89 through 92 Processing sheet with id=AA4, first strand: chain 'JB' and resid 89 through 92 Processing sheet with id=AA5, first strand: chain 'KB' and resid 89 through 92 Processing sheet with id=AA6, first strand: chain 'LB' and resid 89 through 92 Processing sheet with id=AA7, first strand: chain 'MB' and resid 89 through 92 Processing sheet with id=AA8, first strand: chain 'NB' and resid 89 through 92 Processing sheet with id=AA9, first strand: chain 'OB' and resid 89 through 92 Processing sheet with id=AB1, first strand: chain 'PB' and resid 89 through 92 Processing sheet with id=AB2, first strand: chain 'QB' and resid 89 through 92 Processing sheet with id=AB3, first strand: chain 'RB' and resid 89 through 92 Processing sheet with id=AB4, first strand: chain 'SB' and resid 89 through 92 Processing sheet with id=AB5, first strand: chain 'TB' and resid 89 through 92 Processing sheet with id=AB6, first strand: chain 'UB' and resid 89 through 92 Processing sheet with id=AB7, first strand: chain 'VB' and resid 89 through 92 Processing sheet with id=AB8, first strand: chain 'AB' and resid 89 through 92 Processing sheet with id=AB9, first strand: chain 'BB' and resid 89 through 92 Processing sheet with id=AC1, first strand: chain 'CB' and resid 89 through 92 Processing sheet with id=AC2, first strand: chain 'DB' and resid 89 through 92 Processing sheet with id=AC3, first strand: chain 'EB' and resid 89 through 92 Processing sheet with id=AC4, first strand: chain 'FB' and resid 89 through 92 1110 hydrogen bonds defined for protein. 3102 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: 3.26 Time building geometry restraints manager: 2.61 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 7106 1.34 - 1.46: 5025 1.46 - 1.58: 10221 1.58 - 1.70: 0 1.70 - 1.81: 176 Bond restraints: 22528 Sorted by residual: bond pdb=" CB METVA 14 " pdb=" CG METVA 14 " ideal model delta sigma weight residual 1.520 1.490 0.030 3.00e-02 1.11e+03 1.02e+00 bond pdb=" SD METVA 14 " pdb=" CE METVA 14 " ideal model delta sigma weight residual 1.791 1.772 0.019 2.50e-02 1.60e+03 5.72e-01 bond pdb=" CA ILEEB 115 " pdb=" C ILEEB 115 " ideal model delta sigma weight residual 1.530 1.522 0.008 1.12e-02 7.97e+03 4.84e-01 bond pdb=" CB METEA 14 " pdb=" CG METEA 14 " ideal model delta sigma weight residual 1.520 1.539 -0.019 3.00e-02 1.11e+03 4.15e-01 bond pdb=" CA ASPFA 60 " pdb=" CB ASPFA 60 " ideal model delta sigma weight residual 1.529 1.540 -0.010 1.63e-02 3.76e+03 4.04e-01 ... (remaining 22523 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 30572 2.47 - 4.94: 134 4.94 - 7.41: 3 7.41 - 9.88: 2 9.88 - 12.35: 1 Bond angle restraints: 30712 Sorted by residual: angle pdb=" CB METVA 14 " pdb=" CG METVA 14 " pdb=" SD METVA 14 " ideal model delta sigma weight residual 112.70 100.35 12.35 3.00e+00 1.11e-01 1.69e+01 angle pdb=" C GLYEB 108 " pdb=" N ASNEB 109 " pdb=" CA ASNEB 109 " ideal model delta sigma weight residual 121.54 126.93 -5.39 1.91e+00 2.74e-01 7.96e+00 angle pdb=" CB METEA 14 " pdb=" CG METEA 14 " pdb=" SD METEA 14 " ideal model delta sigma weight residual 112.70 120.83 -8.13 3.00e+00 1.11e-01 7.34e+00 angle pdb=" CB METFA 14 " pdb=" CG METFA 14 " pdb=" SD METFA 14 " ideal model delta sigma weight residual 112.70 120.60 -7.90 3.00e+00 1.11e-01 6.93e+00 angle pdb=" N LEUFA 10 " pdb=" CA LEUFA 10 " pdb=" C LEUFA 10 " ideal model delta sigma weight residual 113.55 110.46 3.09 1.26e+00 6.30e-01 6.02e+00 ... (remaining 30707 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 12506 17.81 - 35.61: 836 35.61 - 53.42: 169 53.42 - 71.22: 28 71.22 - 89.03: 35 Dihedral angle restraints: 13574 sinusoidal: 4862 harmonic: 8712 Sorted by residual: dihedral pdb=" CA ASNTA 75 " pdb=" C ASNTA 75 " pdb=" N LEUTA 76 " pdb=" CA LEUTA 76 " ideal model delta harmonic sigma weight residual -180.00 -160.40 -19.60 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA ASNEA 75 " pdb=" C ASNEA 75 " pdb=" N LEUEA 76 " pdb=" CA LEUEA 76 " ideal model delta harmonic sigma weight residual 180.00 -161.78 -18.22 0 5.00e+00 4.00e-02 1.33e+01 dihedral pdb=" CA ASNNA 75 " pdb=" C ASNNA 75 " pdb=" N LEUNA 76 " pdb=" CA LEUNA 76 " ideal model delta harmonic sigma weight residual 180.00 164.04 15.96 0 5.00e+00 4.00e-02 1.02e+01 ... (remaining 13571 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 2861 0.039 - 0.077: 858 0.077 - 0.116: 149 0.116 - 0.155: 47 0.155 - 0.194: 1 Chirality restraints: 3916 Sorted by residual: chirality pdb=" CA METVA 14 " pdb=" N METVA 14 " pdb=" C METVA 14 " pdb=" CB METVA 14 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.37e-01 chirality pdb=" CA ILEVB 103 " pdb=" N ILEVB 103 " pdb=" C ILEVB 103 " pdb=" CB ILEVB 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA ILETB 103 " pdb=" N ILETB 103 " pdb=" C ILETB 103 " pdb=" CB ILETB 103 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.28e-01 ... (remaining 3913 not shown) Planarity restraints: 3784 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILEBA 28 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PROBA 29 " -0.071 5.00e-02 4.00e+02 pdb=" CA PROBA 29 " 0.021 5.00e-02 4.00e+02 pdb=" CD PROBA 29 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILERA 28 " -0.024 5.00e-02 4.00e+02 3.70e-02 2.19e+00 pdb=" N PRORA 29 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRORA 29 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRORA 29 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILEEA 28 " 0.023 5.00e-02 4.00e+02 3.49e-02 1.95e+00 pdb=" N PROEA 29 " -0.060 5.00e-02 4.00e+02 pdb=" CA PROEA 29 " 0.018 5.00e-02 4.00e+02 pdb=" CD PROEA 29 " 0.019 5.00e-02 4.00e+02 ... (remaining 3781 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.74: 1447 2.74 - 3.28: 23460 3.28 - 3.82: 35640 3.82 - 4.36: 45377 4.36 - 4.90: 77620 Nonbonded interactions: 183544 Sorted by model distance: nonbonded pdb=" O GLULA 46 " pdb=" OG SERLA 49 " model vdw 2.194 3.040 nonbonded pdb=" OG SERCB 79 " pdb=" N THRCB 80 " model vdw 2.206 3.120 nonbonded pdb=" O GLUQA 46 " pdb=" OG SERQA 49 " model vdw 2.219 3.040 nonbonded pdb=" O GLUEA 46 " pdb=" OG SEREA 49 " model vdw 2.226 3.040 nonbonded pdb=" O GLUFA 46 " pdb=" OG SERFA 49 " model vdw 2.229 3.040 ... (remaining 183539 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 'AA' selection = chain 'BA' selection = chain 'CA' selection = chain 'DA' selection = chain 'EA' selection = chain 'FA' selection = chain 'GA' selection = chain 'HA' selection = chain 'IA' selection = chain 'JA' selection = chain 'KA' selection = chain 'LA' selection = chain 'MA' selection = chain 'NA' selection = chain 'OA' selection = chain 'PA' selection = chain 'QA' selection = chain 'RA' selection = chain 'SA' selection = chain 'TA' selection = chain 'UA' selection = chain 'VA' } ncs_group { reference = chain 'AB' selection = chain 'BB' selection = chain 'CB' selection = chain 'DB' selection = chain 'EB' selection = chain 'FB' selection = chain 'GB' selection = chain 'HB' selection = chain 'IB' selection = chain 'JB' selection = chain 'KB' selection = chain 'LB' selection = chain 'MB' selection = chain 'NB' selection = chain 'OB' selection = chain 'PB' selection = chain 'QB' selection = chain 'RB' selection = chain 'SB' selection = chain 'TB' selection = chain 'UB' selection = chain 'VB' } 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: 4.170 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 17.750 Find NCS groups from input model: 0.390 Set up NCS constraints: 0.090 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:0.960 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9133 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 : 0.002 0.030 22572 Z= 0.094 Angle : 0.449 12.346 30800 Z= 0.249 Chirality : 0.038 0.194 3916 Planarity : 0.003 0.041 3784 Dihedral : 13.684 89.030 7810 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.06 % Favored : 96.87 % Rotamer: Outliers : 0.00 % Allowed : 0.08 % Favored : 99.92 % 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: 0.69 (0.14), residues: 2970 helix: 1.83 (0.15), residues: 1012 sheet: 0.20 (0.19), residues: 660 loop : -0.46 (0.15), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGBA 42 TYR 0.008 0.001 TYRCA 34 PHE 0.004 0.000 PHEOB 140 TRP 0.007 0.001 TRPQB 122 Details of bonding type rmsd covalent geometry : bond 0.00192 (22528) covalent geometry : angle 0.44882 (30712) SS BOND : bond 0.00117 ( 44) SS BOND : angle 0.51813 ( 88) hydrogen bonds : bond 0.12763 ( 1110) hydrogen bonds : angle 4.93168 ( 3102) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 594 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 594 time to evaluate : 0.590 Fit side-chains REVERT: MA 60 ASP cc_start: 0.8382 (t70) cc_final: 0.7984 (t0) REVERT: MA 68 GLU cc_start: 0.8599 (tp30) cc_final: 0.8263 (tp30) REVERT: TA 68 GLU cc_start: 0.8660 (tp30) cc_final: 0.8252 (tp30) REVERT: KB 116 LYS cc_start: 0.9188 (tptm) cc_final: 0.8970 (tppt) REVERT: PB 147 SER cc_start: 0.8203 (m) cc_final: 0.7838 (t) REVERT: TB 127 GLU cc_start: 0.8595 (mp0) cc_final: 0.8320 (mp0) outliers start: 0 outliers final: 0 residues processed: 594 average time/residue: 0.1247 time to fit residues: 117.0008 Evaluate side-chains 526 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 526 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 197 optimal weight: 3.9990 chunk 215 optimal weight: 2.9990 chunk 20 optimal weight: 9.9990 chunk 132 optimal weight: 0.0040 chunk 261 optimal weight: 0.1980 chunk 248 optimal weight: 1.9990 chunk 207 optimal weight: 3.9990 chunk 155 optimal weight: 0.0970 chunk 244 optimal weight: 0.5980 chunk 183 optimal weight: 0.6980 chunk 111 optimal weight: 0.9980 overall best weight: 0.3190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: UB 86 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.055952 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2500 r_free = 0.2500 target = 0.043582 restraints weight = 54830.563| |-----------------------------------------------------------------------------| r_work (start): 0.2499 rms_B_bonded: 2.25 r_work: 0.2382 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2257 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9263 moved from start: 0.0960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 22572 Z= 0.085 Angle : 0.430 6.817 30800 Z= 0.230 Chirality : 0.038 0.162 3916 Planarity : 0.003 0.044 3784 Dihedral : 3.911 52.084 3146 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.46 % Favored : 97.51 % Rotamer: Outliers : 0.55 % Allowed : 7.11 % Favored : 92.34 % 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: 1.06 (0.15), residues: 2970 helix: 2.27 (0.16), residues: 1056 sheet: 0.03 (0.19), residues: 638 loop : -0.23 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGBA 42 TYR 0.010 0.001 TYRIA 34 PHE 0.004 0.000 PHEGB 140 TRP 0.006 0.001 TRPQB 122 Details of bonding type rmsd covalent geometry : bond 0.00172 (22528) covalent geometry : angle 0.43027 (30712) SS BOND : bond 0.00071 ( 44) SS BOND : angle 0.49178 ( 88) hydrogen bonds : bond 0.03309 ( 1110) hydrogen bonds : angle 3.67896 ( 3102) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 601 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 588 time to evaluate : 0.700 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8922 (t70) cc_final: 0.8624 (t0) REVERT: KA 62 LYS cc_start: 0.9353 (mttt) cc_final: 0.9128 (mtpp) REVERT: LA 55 GLU cc_start: 0.9415 (tp30) cc_final: 0.9175 (tp30) REVERT: LA 60 ASP cc_start: 0.9042 (t70) cc_final: 0.8485 (t0) REVERT: MA 55 GLU cc_start: 0.9490 (tp30) cc_final: 0.9231 (tp30) REVERT: MA 60 ASP cc_start: 0.8867 (t70) cc_final: 0.8473 (t0) REVERT: MA 68 GLU cc_start: 0.9015 (tp30) cc_final: 0.8640 (tp30) REVERT: NA 55 GLU cc_start: 0.9551 (tp30) cc_final: 0.9222 (tp30) REVERT: TA 68 GLU cc_start: 0.9182 (tp30) cc_final: 0.8733 (tp30) REVERT: JB 99 GLU cc_start: 0.8851 (mt-10) cc_final: 0.8641 (mt-10) REVERT: KB 116 LYS cc_start: 0.9233 (tptm) cc_final: 0.9019 (tppt) REVERT: PB 147 SER cc_start: 0.8433 (m) cc_final: 0.8019 (t) REVERT: TB 127 GLU cc_start: 0.9173 (mp0) cc_final: 0.8817 (mp0) outliers start: 13 outliers final: 8 residues processed: 591 average time/residue: 0.1250 time to fit residues: 117.1409 Evaluate side-chains 554 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 546 time to evaluate : 0.593 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 35 ILE Chi-restraints excluded: chain HA residue 52 THR Chi-restraints excluded: chain HA residue 53 VAL Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain KA residue 69 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 73 ASN Chi-restraints excluded: chain TA residue 14 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 88 optimal weight: 0.6980 chunk 106 optimal weight: 0.6980 chunk 222 optimal weight: 4.9990 chunk 257 optimal weight: 3.9990 chunk 285 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 147 optimal weight: 8.9990 chunk 139 optimal weight: 6.9990 chunk 142 optimal weight: 0.0470 chunk 98 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: KA 66 ASN HB 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2817 r_free = 0.2817 target = 0.055368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2484 r_free = 0.2484 target = 0.042953 restraints weight = 55062.861| |-----------------------------------------------------------------------------| r_work (start): 0.2484 rms_B_bonded: 2.26 r_work: 0.2367 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2242 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.2242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9274 moved from start: 0.1102 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 22572 Z= 0.089 Angle : 0.430 7.100 30800 Z= 0.229 Chirality : 0.038 0.150 3916 Planarity : 0.003 0.042 3784 Dihedral : 3.838 46.267 3146 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 0.67 % Allowed : 9.26 % Favored : 90.07 % 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: 1.19 (0.15), residues: 2970 helix: 2.41 (0.16), residues: 1056 sheet: 0.11 (0.19), residues: 638 loop : -0.18 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGBA 42 TYR 0.009 0.001 TYRIA 34 PHE 0.003 0.000 PHEOB 140 TRP 0.007 0.001 TRPRB 122 Details of bonding type rmsd covalent geometry : bond 0.00193 (22528) covalent geometry : angle 0.42937 (30712) SS BOND : bond 0.00091 ( 44) SS BOND : angle 0.53305 ( 88) hydrogen bonds : bond 0.03143 ( 1110) hydrogen bonds : angle 3.55827 ( 3102) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 573 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 557 time to evaluate : 0.722 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8949 (t70) cc_final: 0.8648 (t0) REVERT: LA 55 GLU cc_start: 0.9432 (tp30) cc_final: 0.9160 (tp30) REVERT: LA 60 ASP cc_start: 0.9064 (t70) cc_final: 0.8492 (t0) REVERT: MA 55 GLU cc_start: 0.9509 (tp30) cc_final: 0.9212 (tp30) REVERT: MA 60 ASP cc_start: 0.8904 (t70) cc_final: 0.8493 (t0) REVERT: NA 55 GLU cc_start: 0.9583 (tp30) cc_final: 0.9217 (tp30) REVERT: OA 60 ASP cc_start: 0.9299 (m-30) cc_final: 0.8652 (t0) REVERT: QA 68 GLU cc_start: 0.9082 (tp30) cc_final: 0.8788 (tp30) REVERT: TA 68 GLU cc_start: 0.9190 (tp30) cc_final: 0.8741 (tp30) REVERT: HB 124 ARG cc_start: 0.8935 (ttt-90) cc_final: 0.8715 (ttt-90) REVERT: IB 109 ASN cc_start: 0.8839 (t0) cc_final: 0.8405 (t0) REVERT: JB 99 GLU cc_start: 0.8866 (mt-10) cc_final: 0.8635 (mt-10) REVERT: KB 116 LYS cc_start: 0.9220 (tptm) cc_final: 0.9007 (tppt) REVERT: PB 147 SER cc_start: 0.8418 (m) cc_final: 0.7997 (t) REVERT: TB 127 GLU cc_start: 0.9185 (mp0) cc_final: 0.8822 (mp0) outliers start: 16 outliers final: 10 residues processed: 560 average time/residue: 0.1365 time to fit residues: 120.9059 Evaluate side-chains 546 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 536 time to evaluate : 0.767 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 35 ILE Chi-restraints excluded: chain HA residue 53 VAL Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 53 VAL Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 69 LEU Chi-restraints excluded: chain TA residue 14 MET Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 231 optimal weight: 6.9990 chunk 137 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 272 optimal weight: 2.9990 chunk 180 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 chunk 207 optimal weight: 8.9990 chunk 266 optimal weight: 3.9990 chunk 245 optimal weight: 2.9990 chunk 61 optimal weight: 0.6980 chunk 132 optimal weight: 3.9990 overall best weight: 1.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: KA 66 ASN UB 86 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.053152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2405 r_free = 0.2405 target = 0.040606 restraints weight = 55429.934| |-----------------------------------------------------------------------------| r_work (start): 0.2405 rms_B_bonded: 2.33 r_work: 0.2283 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.2155 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.2155 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9318 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 22572 Z= 0.149 Angle : 0.472 7.707 30800 Z= 0.253 Chirality : 0.040 0.151 3916 Planarity : 0.003 0.044 3784 Dihedral : 4.096 40.419 3146 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.27 % Rotamer: Outliers : 0.72 % Allowed : 10.77 % Favored : 88.51 % 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: 1.14 (0.15), residues: 2970 helix: 2.44 (0.16), residues: 1034 sheet: 0.22 (0.19), residues: 660 loop : -0.33 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGDB 124 TYR 0.011 0.001 TYRIA 34 PHE 0.005 0.001 PHEEB 140 TRP 0.007 0.001 TRPJB 122 Details of bonding type rmsd covalent geometry : bond 0.00349 (22528) covalent geometry : angle 0.47072 (30712) SS BOND : bond 0.00150 ( 44) SS BOND : angle 0.73138 ( 88) hydrogen bonds : bond 0.03537 ( 1110) hydrogen bonds : angle 3.78485 ( 3102) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 522 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 505 time to evaluate : 0.821 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9010 (t70) cc_final: 0.8721 (t0) REVERT: LA 60 ASP cc_start: 0.9143 (t70) cc_final: 0.8543 (t0) REVERT: MA 55 GLU cc_start: 0.9520 (tp30) cc_final: 0.9181 (tp30) REVERT: MA 60 ASP cc_start: 0.8955 (t70) cc_final: 0.8550 (t0) REVERT: NA 55 GLU cc_start: 0.9572 (tp30) cc_final: 0.9142 (tp30) REVERT: NA 60 ASP cc_start: 0.8915 (t0) cc_final: 0.8702 (t0) REVERT: OA 60 ASP cc_start: 0.9316 (m-30) cc_final: 0.8660 (t0) REVERT: PA 60 ASP cc_start: 0.9097 (t70) cc_final: 0.8801 (t0) REVERT: QA 68 GLU cc_start: 0.9132 (tp30) cc_final: 0.8842 (tp30) REVERT: TA 68 GLU cc_start: 0.9180 (tp30) cc_final: 0.8841 (tp30) REVERT: EA 60 ASP cc_start: 0.9294 (t0) cc_final: 0.8747 (t70) REVERT: HB 124 ARG cc_start: 0.8915 (ttt-90) cc_final: 0.8678 (ttt-90) REVERT: IB 109 ASN cc_start: 0.8972 (t0) cc_final: 0.8545 (t0) REVERT: IB 127 GLU cc_start: 0.9147 (mp0) cc_final: 0.8946 (pm20) REVERT: JB 99 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8548 (mt-10) REVERT: PB 147 SER cc_start: 0.8368 (m) cc_final: 0.7926 (t) REVERT: QB 127 GLU cc_start: 0.9195 (mm-30) cc_final: 0.8978 (mp0) REVERT: TB 127 GLU cc_start: 0.9236 (mp0) cc_final: 0.8848 (mp0) outliers start: 17 outliers final: 14 residues processed: 510 average time/residue: 0.1334 time to fit residues: 107.7423 Evaluate side-chains 512 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 498 time to evaluate : 0.673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain HA residue 35 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 53 VAL Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain NA residue 69 LEU Chi-restraints excluded: chain RA residue 45 SER Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain BB residue 137 GLU Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 215 optimal weight: 2.9990 chunk 7 optimal weight: 5.9990 chunk 244 optimal weight: 0.0370 chunk 87 optimal weight: 0.9980 chunk 129 optimal weight: 0.7980 chunk 266 optimal weight: 1.9990 chunk 252 optimal weight: 7.9990 chunk 278 optimal weight: 8.9990 chunk 91 optimal weight: 3.9990 chunk 275 optimal weight: 5.9990 chunk 242 optimal weight: 1.9990 overall best weight: 1.1662 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2767 r_free = 0.2767 target = 0.053846 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2426 r_free = 0.2426 target = 0.041322 restraints weight = 54935.247| |-----------------------------------------------------------------------------| r_work (start): 0.2425 rms_B_bonded: 2.32 r_work: 0.2301 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2175 rms_B_bonded: 4.29 restraints_weight: 0.2500 r_work (final): 0.2175 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9306 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 22572 Z= 0.112 Angle : 0.453 10.324 30800 Z= 0.243 Chirality : 0.039 0.152 3916 Planarity : 0.003 0.047 3784 Dihedral : 4.059 37.764 3146 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.36 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 0.76 % Allowed : 11.70 % Favored : 87.54 % 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: 1.10 (0.15), residues: 2970 helix: 2.27 (0.16), residues: 1056 sheet: 0.19 (0.19), residues: 660 loop : -0.25 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGDB 124 TYR 0.010 0.001 TYRIA 34 PHE 0.003 0.000 PHEPB 140 TRP 0.007 0.001 TRPAB 122 Details of bonding type rmsd covalent geometry : bond 0.00258 (22528) covalent geometry : angle 0.45239 (30712) SS BOND : bond 0.00106 ( 44) SS BOND : angle 0.62976 ( 88) hydrogen bonds : bond 0.03283 ( 1110) hydrogen bonds : angle 3.70347 ( 3102) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 539 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 521 time to evaluate : 0.599 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9006 (t70) cc_final: 0.8712 (t0) REVERT: LA 60 ASP cc_start: 0.9152 (t70) cc_final: 0.8554 (t0) REVERT: MA 55 GLU cc_start: 0.9513 (tp30) cc_final: 0.9183 (tp30) REVERT: MA 60 ASP cc_start: 0.8947 (t70) cc_final: 0.8525 (t0) REVERT: NA 55 GLU cc_start: 0.9584 (tp30) cc_final: 0.9213 (tp30) REVERT: OA 60 ASP cc_start: 0.9292 (m-30) cc_final: 0.8643 (t0) REVERT: PA 60 ASP cc_start: 0.9111 (t70) cc_final: 0.8813 (t0) REVERT: QA 68 GLU cc_start: 0.9123 (tp30) cc_final: 0.8828 (tp30) REVERT: TA 68 GLU cc_start: 0.9185 (tp30) cc_final: 0.8847 (tp30) REVERT: EA 60 ASP cc_start: 0.9307 (t0) cc_final: 0.8732 (t70) REVERT: HB 124 ARG cc_start: 0.8900 (ttt-90) cc_final: 0.8666 (ttt-90) REVERT: IB 109 ASN cc_start: 0.8937 (t0) cc_final: 0.8474 (t0) REVERT: JB 99 GLU cc_start: 0.8833 (mt-10) cc_final: 0.8526 (mt-10) REVERT: PB 147 SER cc_start: 0.8366 (m) cc_final: 0.7912 (t) REVERT: QB 127 GLU cc_start: 0.9191 (mm-30) cc_final: 0.8986 (mp0) REVERT: TB 127 GLU cc_start: 0.9224 (mp0) cc_final: 0.8850 (mp0) outliers start: 18 outliers final: 15 residues processed: 529 average time/residue: 0.1336 time to fit residues: 113.1139 Evaluate side-chains 526 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 511 time to evaluate : 0.888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain HA residue 35 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 53 VAL Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 11 ILE Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain NA residue 69 LEU Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 185 optimal weight: 0.0970 chunk 49 optimal weight: 0.0470 chunk 87 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 246 optimal weight: 6.9990 chunk 245 optimal weight: 0.7980 chunk 141 optimal weight: 2.9990 chunk 128 optimal weight: 3.9990 chunk 229 optimal weight: 4.9990 chunk 75 optimal weight: 2.9990 chunk 162 optimal weight: 9.9990 overall best weight: 1.1880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.053477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2423 r_free = 0.2423 target = 0.041052 restraints weight = 55453.616| |-----------------------------------------------------------------------------| r_work (start): 0.2423 rms_B_bonded: 2.25 r_work: 0.2302 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2176 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2176 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9306 moved from start: 0.1296 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 22572 Z= 0.114 Angle : 0.454 9.488 30800 Z= 0.243 Chirality : 0.039 0.162 3916 Planarity : 0.003 0.046 3784 Dihedral : 4.041 36.988 3146 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 1.14 % Allowed : 12.04 % Favored : 86.83 % 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: 1.10 (0.15), residues: 2970 helix: 2.26 (0.16), residues: 1056 sheet: 0.17 (0.19), residues: 660 loop : -0.23 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARGGB 124 TYR 0.010 0.001 TYRIA 34 PHE 0.003 0.000 PHEEB 140 TRP 0.007 0.001 TRPAB 122 Details of bonding type rmsd covalent geometry : bond 0.00262 (22528) covalent geometry : angle 0.45303 (30712) SS BOND : bond 0.00102 ( 44) SS BOND : angle 0.63257 ( 88) hydrogen bonds : bond 0.03259 ( 1110) hydrogen bonds : angle 3.68836 ( 3102) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 518 time to evaluate : 0.695 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8997 (t70) cc_final: 0.8696 (t0) REVERT: HA 77 LEU cc_start: 0.8213 (tp) cc_final: 0.7976 (tp) REVERT: LA 60 ASP cc_start: 0.9169 (t70) cc_final: 0.8568 (t0) REVERT: MA 55 GLU cc_start: 0.9516 (tp30) cc_final: 0.9179 (tp30) REVERT: MA 60 ASP cc_start: 0.8939 (t70) cc_final: 0.8523 (t0) REVERT: NA 55 GLU cc_start: 0.9571 (tp30) cc_final: 0.9214 (tp30) REVERT: OA 60 ASP cc_start: 0.9306 (m-30) cc_final: 0.8654 (t0) REVERT: PA 60 ASP cc_start: 0.9115 (t70) cc_final: 0.8790 (t0) REVERT: QA 55 GLU cc_start: 0.9468 (tp30) cc_final: 0.9104 (tp30) REVERT: QA 68 GLU cc_start: 0.9118 (tp30) cc_final: 0.8825 (tp30) REVERT: TA 68 GLU cc_start: 0.9201 (tp30) cc_final: 0.8858 (tp30) REVERT: VA 14 MET cc_start: 0.9620 (mmm) cc_final: 0.9358 (mmm) REVERT: EA 60 ASP cc_start: 0.9315 (t0) cc_final: 0.8711 (t70) REVERT: HB 124 ARG cc_start: 0.8884 (ttt-90) cc_final: 0.8647 (ttt-90) REVERT: JB 99 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8530 (mt-10) REVERT: PB 147 SER cc_start: 0.8368 (m) cc_final: 0.7906 (t) REVERT: QB 127 GLU cc_start: 0.9206 (mm-30) cc_final: 0.8995 (mp0) REVERT: TB 127 GLU cc_start: 0.9193 (mp0) cc_final: 0.8804 (mp0) outliers start: 27 outliers final: 21 residues processed: 533 average time/residue: 0.1250 time to fit residues: 105.7216 Evaluate side-chains 525 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 504 time to evaluate : 0.626 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 53 VAL Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 11 ILE Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain NA residue 69 LEU Chi-restraints excluded: chain RA residue 45 SER Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain IB residue 83 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain BB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 68 optimal weight: 0.0040 chunk 206 optimal weight: 0.9990 chunk 259 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 5.9990 chunk 194 optimal weight: 0.0020 chunk 192 optimal weight: 3.9990 chunk 277 optimal weight: 6.9990 chunk 160 optimal weight: 0.0000 chunk 235 optimal weight: 5.9990 chunk 247 optimal weight: 5.9990 overall best weight: 0.3806 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.055742 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2493 r_free = 0.2493 target = 0.043351 restraints weight = 54766.945| |-----------------------------------------------------------------------------| r_work (start): 0.2490 rms_B_bonded: 2.25 r_work: 0.2372 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2248 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9270 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 22572 Z= 0.081 Angle : 0.437 8.546 30800 Z= 0.233 Chirality : 0.038 0.164 3916 Planarity : 0.003 0.043 3784 Dihedral : 3.819 35.759 3146 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 3.92 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 1.09 % Allowed : 12.04 % Favored : 86.87 % 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: 1.20 (0.15), residues: 2970 helix: 2.36 (0.16), residues: 1056 sheet: 0.27 (0.21), residues: 572 loop : -0.20 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARGBA 42 TYR 0.011 0.001 TYRRA 34 PHE 0.003 0.000 PHEHB 107 TRP 0.008 0.001 TRPQB 122 Details of bonding type rmsd covalent geometry : bond 0.00172 (22528) covalent geometry : angle 0.43717 (30712) SS BOND : bond 0.00094 ( 44) SS BOND : angle 0.47732 ( 88) hydrogen bonds : bond 0.02874 ( 1110) hydrogen bonds : angle 3.50194 ( 3102) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 590 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 564 time to evaluate : 1.125 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8974 (t70) cc_final: 0.8691 (t0) REVERT: HA 55 GLU cc_start: 0.9113 (tp30) cc_final: 0.8881 (tp30) REVERT: HA 77 LEU cc_start: 0.8237 (tp) cc_final: 0.8022 (tp) REVERT: LA 60 ASP cc_start: 0.9133 (t70) cc_final: 0.8536 (t0) REVERT: MA 55 GLU cc_start: 0.9521 (tp30) cc_final: 0.9207 (tp30) REVERT: MA 60 ASP cc_start: 0.8927 (t70) cc_final: 0.8499 (t0) REVERT: MA 68 GLU cc_start: 0.9047 (tp30) cc_final: 0.8824 (tp30) REVERT: NA 55 GLU cc_start: 0.9573 (tp30) cc_final: 0.9298 (tp30) REVERT: NA 69 LEU cc_start: 0.8536 (OUTLIER) cc_final: 0.8308 (mp) REVERT: OA 60 ASP cc_start: 0.9287 (m-30) cc_final: 0.8701 (t0) REVERT: PA 60 ASP cc_start: 0.9103 (t70) cc_final: 0.8768 (t0) REVERT: QA 55 GLU cc_start: 0.9491 (tp30) cc_final: 0.9133 (tp30) REVERT: QA 68 GLU cc_start: 0.9111 (tp30) cc_final: 0.8816 (tp30) REVERT: SA 55 GLU cc_start: 0.9362 (tp30) cc_final: 0.9058 (tp30) REVERT: TA 68 GLU cc_start: 0.9208 (tp30) cc_final: 0.8719 (tp30) REVERT: VA 14 MET cc_start: 0.9628 (mmm) cc_final: 0.9360 (mmm) REVERT: EA 60 ASP cc_start: 0.9287 (t0) cc_final: 0.8686 (t70) REVERT: IB 109 ASN cc_start: 0.8911 (t0) cc_final: 0.8424 (t0) REVERT: JB 99 GLU cc_start: 0.8819 (mt-10) cc_final: 0.8490 (mt-10) REVERT: PB 147 SER cc_start: 0.8369 (m) cc_final: 0.7908 (t) REVERT: TB 127 GLU cc_start: 0.9165 (mp0) cc_final: 0.8808 (mp0) outliers start: 26 outliers final: 13 residues processed: 578 average time/residue: 0.1524 time to fit residues: 141.5419 Evaluate side-chains 559 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 545 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain IA residue 53 VAL Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain NA residue 69 LEU Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain IB residue 83 VAL Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 22 optimal weight: 1.9990 chunk 206 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 68 optimal weight: 0.0980 chunk 226 optimal weight: 8.9990 chunk 262 optimal weight: 9.9990 chunk 56 optimal weight: 0.9990 chunk 57 optimal weight: 0.8980 chunk 65 optimal weight: 0.9980 chunk 165 optimal weight: 10.0000 chunk 179 optimal weight: 5.9990 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2804 r_free = 0.2804 target = 0.055218 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2467 r_free = 0.2467 target = 0.042662 restraints weight = 54418.420| |-----------------------------------------------------------------------------| r_work (start): 0.2465 rms_B_bonded: 2.33 r_work: 0.2345 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2218 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9282 moved from start: 0.1379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 22572 Z= 0.093 Angle : 0.450 8.252 30800 Z= 0.238 Chirality : 0.038 0.163 3916 Planarity : 0.003 0.043 3784 Dihedral : 3.807 35.808 3146 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.73 % Favored : 97.24 % Rotamer: Outliers : 0.97 % Allowed : 12.58 % Favored : 86.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.22 (0.15), residues: 2970 helix: 2.36 (0.16), residues: 1056 sheet: 0.26 (0.20), residues: 616 loop : -0.17 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGHB 124 TYR 0.009 0.001 TYRIA 34 PHE 0.003 0.000 PHEGB 140 TRP 0.006 0.001 TRPJB 122 Details of bonding type rmsd covalent geometry : bond 0.00211 (22528) covalent geometry : angle 0.44917 (30712) SS BOND : bond 0.00093 ( 44) SS BOND : angle 0.57373 ( 88) hydrogen bonds : bond 0.03012 ( 1110) hydrogen bonds : angle 3.52159 ( 3102) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 566 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 543 time to evaluate : 0.926 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8996 (t70) cc_final: 0.8695 (t0) REVERT: HA 55 GLU cc_start: 0.9133 (tp30) cc_final: 0.8909 (tp30) REVERT: HA 77 LEU cc_start: 0.8256 (tp) cc_final: 0.8042 (tp) REVERT: LA 60 ASP cc_start: 0.9157 (t70) cc_final: 0.8549 (t0) REVERT: MA 55 GLU cc_start: 0.9542 (tp30) cc_final: 0.9206 (tp30) REVERT: MA 60 ASP cc_start: 0.8945 (t70) cc_final: 0.8513 (t0) REVERT: NA 55 GLU cc_start: 0.9597 (tp30) cc_final: 0.9268 (tp30) REVERT: NA 69 LEU cc_start: 0.8576 (OUTLIER) cc_final: 0.8335 (mp) REVERT: OA 60 ASP cc_start: 0.9281 (m-30) cc_final: 0.8694 (t0) REVERT: PA 60 ASP cc_start: 0.9128 (t70) cc_final: 0.8793 (t0) REVERT: QA 60 ASP cc_start: 0.8932 (t70) cc_final: 0.8635 (t0) REVERT: QA 68 GLU cc_start: 0.9129 (tp30) cc_final: 0.8830 (tp30) REVERT: TA 68 GLU cc_start: 0.9202 (tp30) cc_final: 0.8711 (tp30) REVERT: EA 60 ASP cc_start: 0.9288 (t0) cc_final: 0.8671 (t70) REVERT: IB 109 ASN cc_start: 0.8952 (t0) cc_final: 0.8471 (t0) REVERT: IB 127 GLU cc_start: 0.8812 (pm20) cc_final: 0.8590 (pm20) REVERT: JB 99 GLU cc_start: 0.8823 (mt-10) cc_final: 0.8481 (mt-10) REVERT: PB 147 SER cc_start: 0.8342 (m) cc_final: 0.7884 (t) REVERT: TB 127 GLU cc_start: 0.9224 (mp0) cc_final: 0.8853 (mp0) REVERT: EB 99 GLU cc_start: 0.8966 (pt0) cc_final: 0.8564 (pm20) outliers start: 23 outliers final: 17 residues processed: 559 average time/residue: 0.1487 time to fit residues: 133.2847 Evaluate side-chains 557 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 539 time to evaluate : 0.932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain IA residue 53 VAL Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain NA residue 69 LEU Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain TA residue 14 MET Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain BB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 63 optimal weight: 0.9980 chunk 191 optimal weight: 3.9990 chunk 246 optimal weight: 7.9990 chunk 129 optimal weight: 0.9990 chunk 238 optimal weight: 7.9990 chunk 53 optimal weight: 5.9990 chunk 17 optimal weight: 1.9990 chunk 251 optimal weight: 2.9990 chunk 43 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 200 optimal weight: 0.9980 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.054906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2454 r_free = 0.2454 target = 0.042294 restraints weight = 54763.290| |-----------------------------------------------------------------------------| r_work (start): 0.2452 rms_B_bonded: 2.34 r_work: 0.2332 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2204 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2204 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9290 moved from start: 0.1393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 22572 Z= 0.101 Angle : 0.463 10.801 30800 Z= 0.244 Chirality : 0.038 0.165 3916 Planarity : 0.003 0.044 3784 Dihedral : 3.847 36.008 3146 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 1.01 % Allowed : 12.84 % Favored : 86.15 % 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: 1.20 (0.15), residues: 2970 helix: 2.34 (0.16), residues: 1056 sheet: 0.25 (0.20), residues: 616 loop : -0.17 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGHB 124 TYR 0.012 0.001 TYRRA 34 PHE 0.003 0.000 PHEEB 140 TRP 0.006 0.001 TRPAB 122 Details of bonding type rmsd covalent geometry : bond 0.00233 (22528) covalent geometry : angle 0.46252 (30712) SS BOND : bond 0.00096 ( 44) SS BOND : angle 0.62196 ( 88) hydrogen bonds : bond 0.03077 ( 1110) hydrogen bonds : angle 3.55965 ( 3102) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 554 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 530 time to evaluate : 0.918 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9024 (t70) cc_final: 0.8711 (t0) REVERT: HA 77 LEU cc_start: 0.8215 (tp) cc_final: 0.8008 (tp) REVERT: LA 60 ASP cc_start: 0.9165 (t70) cc_final: 0.8563 (t0) REVERT: MA 55 GLU cc_start: 0.9548 (tp30) cc_final: 0.9220 (tp30) REVERT: MA 60 ASP cc_start: 0.8935 (t70) cc_final: 0.8496 (t0) REVERT: NA 55 GLU cc_start: 0.9603 (tp30) cc_final: 0.9266 (tp30) REVERT: OA 60 ASP cc_start: 0.9296 (m-30) cc_final: 0.8712 (t0) REVERT: PA 60 ASP cc_start: 0.9123 (t70) cc_final: 0.8780 (t0) REVERT: QA 55 GLU cc_start: 0.9434 (tp30) cc_final: 0.9099 (tp30) REVERT: QA 60 ASP cc_start: 0.8913 (t70) cc_final: 0.8602 (t0) REVERT: QA 68 GLU cc_start: 0.9124 (tp30) cc_final: 0.8828 (tp30) REVERT: SA 55 GLU cc_start: 0.9372 (tp30) cc_final: 0.9056 (tp30) REVERT: TA 68 GLU cc_start: 0.9222 (tp30) cc_final: 0.8739 (tp30) REVERT: EA 60 ASP cc_start: 0.9287 (t0) cc_final: 0.8695 (t70) REVERT: HB 136 VAL cc_start: 0.9355 (p) cc_final: 0.9107 (p) REVERT: IB 109 ASN cc_start: 0.8969 (t0) cc_final: 0.8481 (t0) REVERT: IB 127 GLU cc_start: 0.8823 (pm20) cc_final: 0.8619 (pm20) REVERT: JB 99 GLU cc_start: 0.8820 (mt-10) cc_final: 0.8486 (mt-10) REVERT: PB 147 SER cc_start: 0.8334 (m) cc_final: 0.7866 (t) REVERT: RB 127 GLU cc_start: 0.8906 (mp0) cc_final: 0.8587 (mp0) REVERT: TB 127 GLU cc_start: 0.9230 (mp0) cc_final: 0.8862 (mp0) outliers start: 24 outliers final: 21 residues processed: 546 average time/residue: 0.1520 time to fit residues: 133.3592 Evaluate side-chains 549 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 528 time to evaluate : 0.852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 53 VAL Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain NA residue 69 LEU Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain TA residue 14 MET Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain IB residue 83 VAL Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain BB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain CB residue 83 VAL Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 10 optimal weight: 0.8980 chunk 91 optimal weight: 2.9990 chunk 209 optimal weight: 4.9990 chunk 97 optimal weight: 0.9990 chunk 106 optimal weight: 2.9990 chunk 197 optimal weight: 6.9990 chunk 29 optimal weight: 0.8980 chunk 214 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 57 optimal weight: 1.9990 chunk 213 optimal weight: 1.9990 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.054323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2437 r_free = 0.2437 target = 0.041739 restraints weight = 54984.669| |-----------------------------------------------------------------------------| r_work (start): 0.2438 rms_B_bonded: 2.34 r_work: 0.2316 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2188 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.2188 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9297 moved from start: 0.1403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 22572 Z= 0.112 Angle : 0.471 11.313 30800 Z= 0.248 Chirality : 0.039 0.163 3916 Planarity : 0.003 0.045 3784 Dihedral : 3.913 36.150 3146 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.39 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.01 % Allowed : 13.01 % Favored : 85.98 % 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: 1.17 (0.15), residues: 2970 helix: 2.32 (0.16), residues: 1056 sheet: 0.23 (0.20), residues: 616 loop : -0.19 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGHB 124 TYR 0.012 0.001 TYRRA 34 PHE 0.003 0.000 PHEEB 140 TRP 0.006 0.001 TRPAB 122 Details of bonding type rmsd covalent geometry : bond 0.00260 (22528) covalent geometry : angle 0.46988 (30712) SS BOND : bond 0.00101 ( 44) SS BOND : angle 0.68671 ( 88) hydrogen bonds : bond 0.03198 ( 1110) hydrogen bonds : angle 3.61757 ( 3102) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 5940 Ramachandran restraints generated. 2970 Oldfield, 0 Emsley, 2970 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 551 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 527 time to evaluate : 0.863 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9025 (t70) cc_final: 0.8708 (t0) REVERT: LA 60 ASP cc_start: 0.9164 (t70) cc_final: 0.8552 (t0) REVERT: MA 55 GLU cc_start: 0.9537 (tp30) cc_final: 0.9195 (tp30) REVERT: MA 60 ASP cc_start: 0.8960 (t70) cc_final: 0.8530 (t0) REVERT: NA 55 GLU cc_start: 0.9593 (tp30) cc_final: 0.9213 (tp30) REVERT: OA 60 ASP cc_start: 0.9296 (m-30) cc_final: 0.8641 (t0) REVERT: PA 60 ASP cc_start: 0.9130 (t70) cc_final: 0.8787 (t0) REVERT: QA 55 GLU cc_start: 0.9436 (tp30) cc_final: 0.9077 (tp30) REVERT: QA 60 ASP cc_start: 0.8915 (t70) cc_final: 0.8609 (t0) REVERT: QA 68 GLU cc_start: 0.9113 (tp30) cc_final: 0.8815 (tp30) REVERT: SA 55 GLU cc_start: 0.9371 (tp30) cc_final: 0.9039 (tp30) REVERT: TA 68 GLU cc_start: 0.9212 (tp30) cc_final: 0.8723 (tp30) REVERT: EA 60 ASP cc_start: 0.9275 (t0) cc_final: 0.8680 (t70) REVERT: IB 109 ASN cc_start: 0.8986 (t0) cc_final: 0.8487 (t0) REVERT: IB 127 GLU cc_start: 0.8837 (pm20) cc_final: 0.8625 (pm20) REVERT: JB 99 GLU cc_start: 0.8801 (mt-10) cc_final: 0.8462 (mt-10) REVERT: PB 147 SER cc_start: 0.8340 (m) cc_final: 0.7860 (t) REVERT: RB 127 GLU cc_start: 0.8942 (mp0) cc_final: 0.8650 (mp0) REVERT: TB 127 GLU cc_start: 0.9237 (mp0) cc_final: 0.8869 (mp0) outliers start: 24 outliers final: 22 residues processed: 544 average time/residue: 0.1505 time to fit residues: 130.8487 Evaluate side-chains 548 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 526 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain NA residue 52 THR Chi-restraints excluded: chain NA residue 69 LEU Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain IB residue 83 VAL Chi-restraints excluded: chain JB residue 83 VAL Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain NB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain VB residue 83 VAL Chi-restraints excluded: chain BB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain CB residue 83 VAL Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain EB residue 147 SER Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 150 optimal weight: 0.8980 chunk 15 optimal weight: 2.9990 chunk 29 optimal weight: 0.2980 chunk 48 optimal weight: 4.9990 chunk 261 optimal weight: 4.9990 chunk 177 optimal weight: 5.9990 chunk 259 optimal weight: 0.9990 chunk 173 optimal weight: 9.9990 chunk 46 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 197 optimal weight: 6.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2775 r_free = 0.2775 target = 0.053892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2435 r_free = 0.2435 target = 0.041444 restraints weight = 55262.227| |-----------------------------------------------------------------------------| r_work (start): 0.2434 rms_B_bonded: 2.26 r_work: 0.2314 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2190 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.2190 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9302 moved from start: 0.1413 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 22572 Z= 0.117 Angle : 0.481 10.961 30800 Z= 0.254 Chirality : 0.039 0.161 3916 Planarity : 0.003 0.045 3784 Dihedral : 3.963 36.155 3146 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % Rotamer: Outliers : 0.93 % Allowed : 13.38 % Favored : 85.69 % 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: 1.13 (0.15), residues: 2970 helix: 2.28 (0.16), residues: 1056 sheet: 0.22 (0.20), residues: 616 loop : -0.22 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARGHB 124 TYR 0.013 0.001 TYRIB 93 PHE 0.003 0.001 PHEEB 140 TRP 0.006 0.001 TRPAB 122 Details of bonding type rmsd covalent geometry : bond 0.00272 (22528) covalent geometry : angle 0.47965 (30712) SS BOND : bond 0.00113 ( 44) SS BOND : angle 0.73368 ( 88) hydrogen bonds : bond 0.03244 ( 1110) hydrogen bonds : angle 3.64762 ( 3102) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5497.57 seconds wall clock time: 95 minutes 6.95 seconds (5706.95 seconds total)