Starting phenix.real_space_refine on Thu Jun 19 04:48:35 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8tob_41442/06_2025/8tob_41442.cif Found real_map, /net/cci-nas-00/data/ceres_data/8tob_41442/06_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8tob_41442/06_2025/8tob_41442.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8tob_41442/06_2025/8tob_41442.map" model { file = "/net/cci-nas-00/data/ceres_data/8tob_41442/06_2025/8tob_41442.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8tob_41442/06_2025/8tob_41442.cif" } resolution = 3.14 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.010 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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 13.83, per 1000 atoms: 0.62 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: 4.88 Conformation dependent library (CDL) restraints added in 2.8 seconds 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: 2.08 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: 7.08 Time building geometry restraints manager: 5.91 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: 0.01 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: 4.150 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.790 Check model and map are aligned: 0.150 Set scattering table: 0.190 Process input model: 47.370 Find NCS groups from input model: 0.890 Set up NCS constraints: 0.180 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 56.540 ------------------------------------------------------------------------------- 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 : 4.63 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 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 TRP 0.007 0.001 TRPQB 122 PHE 0.004 0.000 PHEOB 140 TYR 0.008 0.001 TYRCA 34 ARG 0.004 0.000 ARGBA 42 Details of bonding type rmsd hydrogen bonds : bond 0.12763 ( 1110) hydrogen bonds : angle 4.93168 ( 3102) SS BOND : bond 0.00117 ( 44) SS BOND : angle 0.51813 ( 88) covalent geometry : bond 0.00192 (22528) covalent geometry : angle 0.44882 (30712) *********************** 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 : 2.799 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: 0.3143 time to fit residues: 292.6360 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 : 2.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 241 optimal weight: 4.9990 chunk 216 optimal weight: 7.9990 chunk 120 optimal weight: 0.0170 chunk 74 optimal weight: 0.7980 chunk 146 optimal weight: 8.9990 chunk 115 optimal weight: 0.5980 chunk 224 optimal weight: 6.9990 chunk 86 optimal weight: 0.9980 chunk 136 optimal weight: 6.9990 chunk 166 optimal weight: 20.0000 chunk 259 optimal weight: 6.9990 overall best weight: 1.4820 ------------------------------------------------------------------------------- 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 = 0.2759 r_free = 0.2759 target = 0.053223 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2420 r_free = 0.2420 target = 0.040864 restraints weight = 55285.191| |-----------------------------------------------------------------------------| r_work (start): 0.2418 rms_B_bonded: 2.24 r_work: 0.2298 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2172 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9310 moved from start: 0.0926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 22572 Z= 0.136 Angle : 0.469 7.262 30800 Z= 0.252 Chirality : 0.040 0.167 3916 Planarity : 0.004 0.048 3784 Dihedral : 4.162 52.655 3146 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.56 % Favored : 97.41 % Rotamer: Outliers : 0.63 % Allowed : 7.20 % Favored : 92.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 2970 helix: 2.17 (0.16), residues: 1056 sheet: 0.15 (0.19), residues: 660 loop : -0.34 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAB 122 PHE 0.005 0.001 PHEEB 140 TYR 0.008 0.001 TYRIA 34 ARG 0.004 0.000 ARGBA 42 Details of bonding type rmsd hydrogen bonds : bond 0.03678 ( 1110) hydrogen bonds : angle 3.90983 ( 3102) SS BOND : bond 0.00100 ( 44) SS BOND : angle 0.69233 ( 88) covalent geometry : bond 0.00316 (22528) covalent geometry : angle 0.46785 (30712) *********************** 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 540 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 525 time to evaluate : 2.655 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8968 (t70) cc_final: 0.8679 (t0) REVERT: KA 62 LYS cc_start: 0.9402 (mttt) cc_final: 0.9181 (mtpp) REVERT: LA 55 GLU cc_start: 0.9400 (tp30) cc_final: 0.9163 (tp30) REVERT: LA 60 ASP cc_start: 0.9059 (t70) cc_final: 0.8523 (t0) REVERT: MA 60 ASP cc_start: 0.8878 (t70) cc_final: 0.8508 (t0) REVERT: NA 60 ASP cc_start: 0.8954 (t0) cc_final: 0.8728 (t0) REVERT: TA 68 GLU cc_start: 0.9178 (tp30) cc_final: 0.8849 (tp30) REVERT: JB 99 GLU cc_start: 0.8792 (mt-10) cc_final: 0.8574 (mt-10) REVERT: KB 116 LYS cc_start: 0.9260 (tptm) cc_final: 0.9019 (tppt) REVERT: PB 147 SER cc_start: 0.8443 (m) cc_final: 0.8016 (t) REVERT: QB 127 GLU cc_start: 0.9216 (mm-30) cc_final: 0.8994 (mp0) REVERT: TB 127 GLU cc_start: 0.9185 (mp0) cc_final: 0.8795 (mp0) outliers start: 15 outliers final: 11 residues processed: 528 average time/residue: 0.3233 time to fit residues: 266.6576 Evaluate side-chains 516 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 505 time to evaluate : 2.481 ------------------------------------------------------------------------------- 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 RA residue 56 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 14 MET Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain EB residue 147 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 242 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 125 optimal weight: 7.9990 chunk 18 optimal weight: 3.9990 chunk 61 optimal weight: 2.9990 chunk 132 optimal weight: 5.9990 chunk 221 optimal weight: 6.9990 chunk 231 optimal weight: 6.9990 chunk 234 optimal weight: 4.9990 chunk 74 optimal weight: 5.9990 chunk 116 optimal weight: 0.6980 overall best weight: 2.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: HB 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2719 r_free = 0.2719 target = 0.051800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2372 r_free = 0.2372 target = 0.039359 restraints weight = 55556.536| |-----------------------------------------------------------------------------| r_work (start): 0.2373 rms_B_bonded: 2.22 r_work: 0.2249 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2124 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9335 moved from start: 0.1233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 22572 Z= 0.178 Angle : 0.498 6.922 30800 Z= 0.269 Chirality : 0.041 0.152 3916 Planarity : 0.004 0.048 3784 Dihedral : 4.392 44.624 3146 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 2.76 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 0.97 % Allowed : 9.60 % Favored : 89.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.15), residues: 2970 helix: 2.29 (0.16), residues: 1034 sheet: 0.17 (0.19), residues: 660 loop : -0.45 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPVB 122 PHE 0.005 0.001 PHEPB 140 TYR 0.007 0.001 TYRIA 34 ARG 0.003 0.000 ARGBA 42 Details of bonding type rmsd hydrogen bonds : bond 0.03842 ( 1110) hydrogen bonds : angle 3.97358 ( 3102) SS BOND : bond 0.00149 ( 44) SS BOND : angle 0.76559 ( 88) covalent geometry : bond 0.00419 (22528) covalent geometry : angle 0.49653 (30712) *********************** 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 522 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 499 time to evaluate : 2.371 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8986 (t70) cc_final: 0.8712 (t0) REVERT: HA 75 ASN cc_start: 0.9334 (t0) cc_final: 0.9066 (t0) REVERT: LA 60 ASP cc_start: 0.9077 (t70) cc_final: 0.8546 (t0) REVERT: MA 55 GLU cc_start: 0.9505 (tp30) cc_final: 0.9189 (tp30) REVERT: MA 60 ASP cc_start: 0.8944 (t70) cc_final: 0.8565 (t0) REVERT: NA 60 ASP cc_start: 0.8963 (t0) cc_final: 0.8669 (t0) REVERT: PA 60 ASP cc_start: 0.9072 (t0) cc_final: 0.8846 (t0) REVERT: EA 60 ASP cc_start: 0.8939 (t0) cc_final: 0.8688 (t0) REVERT: HB 124 ARG cc_start: 0.8945 (ttt-90) cc_final: 0.8730 (ttt-90) REVERT: IB 109 ASN cc_start: 0.9008 (t0) cc_final: 0.8536 (t0) REVERT: JB 99 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8559 (mt-10) REVERT: PB 147 SER cc_start: 0.8366 (m) cc_final: 0.7921 (t) REVERT: QB 127 GLU cc_start: 0.9260 (mm-30) cc_final: 0.9007 (mp0) REVERT: TB 127 GLU cc_start: 0.9237 (mp0) cc_final: 0.8853 (mp0) outliers start: 23 outliers final: 19 residues processed: 504 average time/residue: 0.3268 time to fit residues: 257.2387 Evaluate side-chains 504 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 485 time to evaluate : 2.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain GA residue 73 ASN Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain KA residue 52 THR Chi-restraints excluded: chain KA residue 69 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain QA residue 56 THR Chi-restraints excluded: chain QA residue 73 ASN Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain UA residue 56 THR Chi-restraints excluded: chain IB residue 136 VAL Chi-restraints excluded: chain KB residue 110 SER Chi-restraints excluded: chain TB residue 147 SER 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 275 optimal weight: 5.9990 chunk 180 optimal weight: 7.9990 chunk 116 optimal weight: 4.9990 chunk 186 optimal weight: 7.9990 chunk 189 optimal weight: 5.9990 chunk 268 optimal weight: 10.0000 chunk 228 optimal weight: 7.9990 chunk 145 optimal weight: 5.9990 chunk 55 optimal weight: 0.0570 chunk 137 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 overall best weight: 2.5102 ------------------------------------------------------------------------------- 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 = 0.2699 r_free = 0.2699 target = 0.051127 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2349 r_free = 0.2349 target = 0.038691 restraints weight = 56376.927| |-----------------------------------------------------------------------------| r_work (start): 0.2348 rms_B_bonded: 2.23 r_work: 0.2225 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.2100 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.2100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9345 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 22572 Z= 0.207 Angle : 0.510 6.865 30800 Z= 0.276 Chirality : 0.042 0.152 3916 Planarity : 0.004 0.053 3784 Dihedral : 4.543 39.545 3146 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 2.78 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.79 % Favored : 97.17 % Rotamer: Outliers : 1.98 % Allowed : 10.73 % Favored : 87.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.15), residues: 2970 helix: 2.21 (0.16), residues: 1034 sheet: 0.11 (0.19), residues: 660 loop : -0.51 (0.15), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAB 122 PHE 0.005 0.001 PHEEB 140 TYR 0.007 0.001 TYRNA 34 ARG 0.002 0.000 ARGBA 42 Details of bonding type rmsd hydrogen bonds : bond 0.03909 ( 1110) hydrogen bonds : angle 4.03820 ( 3102) SS BOND : bond 0.00161 ( 44) SS BOND : angle 0.83957 ( 88) covalent geometry : bond 0.00490 (22528) covalent geometry : angle 0.50920 (30712) *********************** 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 535 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 488 time to evaluate : 2.404 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9031 (t70) cc_final: 0.8731 (t0) REVERT: LA 60 ASP cc_start: 0.9148 (t70) cc_final: 0.8592 (t0) REVERT: MA 55 GLU cc_start: 0.9538 (tp30) cc_final: 0.9129 (tp30) REVERT: MA 60 ASP cc_start: 0.8943 (t70) cc_final: 0.8553 (t0) REVERT: NA 60 ASP cc_start: 0.9005 (t0) cc_final: 0.8682 (t0) REVERT: PA 60 ASP cc_start: 0.9118 (t0) cc_final: 0.8867 (t0) REVERT: TA 37 LYS cc_start: 0.9534 (OUTLIER) cc_final: 0.9209 (tttm) REVERT: EA 60 ASP cc_start: 0.8986 (t70) cc_final: 0.8700 (t0) REVERT: HB 124 ARG cc_start: 0.8916 (ttt-90) cc_final: 0.8702 (ttt-90) REVERT: JB 99 GLU cc_start: 0.8775 (mt-10) cc_final: 0.8500 (mt-10) REVERT: PB 99 GLU cc_start: 0.9106 (mt-10) cc_final: 0.8899 (pt0) REVERT: QB 127 GLU cc_start: 0.9248 (mm-30) cc_final: 0.8997 (mp0) REVERT: TB 127 GLU cc_start: 0.9243 (mp0) cc_final: 0.8856 (mp0) outliers start: 47 outliers final: 32 residues processed: 510 average time/residue: 0.3183 time to fit residues: 255.0397 Evaluate side-chains 513 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 480 time to evaluate : 2.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain GA residue 73 ASN Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain JA residue 52 THR Chi-restraints excluded: chain KA residue 52 THR Chi-restraints excluded: chain KA residue 69 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 11 ILE Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain QA residue 56 THR Chi-restraints excluded: chain QA residue 73 ASN Chi-restraints excluded: chain RA residue 45 SER Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 37 LYS Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain UA residue 56 THR Chi-restraints excluded: chain VA residue 49 SER Chi-restraints excluded: chain IB residue 136 VAL Chi-restraints excluded: chain JB residue 110 SER Chi-restraints excluded: chain KB residue 110 SER 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 SB residue 147 SER Chi-restraints excluded: chain TB residue 147 SER 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 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 170 optimal weight: 4.9990 chunk 244 optimal weight: 7.9990 chunk 267 optimal weight: 3.9990 chunk 44 optimal weight: 0.9980 chunk 7 optimal weight: 4.9990 chunk 276 optimal weight: 9.9990 chunk 25 optimal weight: 4.9990 chunk 110 optimal weight: 0.7980 chunk 193 optimal weight: 5.9990 chunk 185 optimal weight: 2.9990 chunk 106 optimal weight: 0.8980 overall best weight: 1.9384 ------------------------------------------------------------------------------- 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 = 0.2711 r_free = 0.2711 target = 0.051613 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.039152 restraints weight = 55817.888| |-----------------------------------------------------------------------------| r_work (start): 0.2361 rms_B_bonded: 2.24 r_work: 0.2239 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2113 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.2113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9338 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22572 Z= 0.166 Angle : 0.493 10.181 30800 Z= 0.266 Chirality : 0.040 0.152 3916 Planarity : 0.003 0.052 3784 Dihedral : 4.495 38.360 3146 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.93 % Favored : 97.04 % Rotamer: Outliers : 1.81 % Allowed : 11.87 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.87 (0.15), residues: 2970 helix: 2.22 (0.16), residues: 1034 sheet: 0.09 (0.19), residues: 660 loop : -0.50 (0.15), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRPAB 122 PHE 0.004 0.001 PHESB 140 TYR 0.007 0.001 TYRIA 34 ARG 0.001 0.000 ARGSB 124 Details of bonding type rmsd hydrogen bonds : bond 0.03694 ( 1110) hydrogen bonds : angle 3.95983 ( 3102) SS BOND : bond 0.00143 ( 44) SS BOND : angle 0.76624 ( 88) covalent geometry : bond 0.00391 (22528) covalent geometry : angle 0.49163 (30712) *********************** 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 536 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 493 time to evaluate : 3.546 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9044 (t70) cc_final: 0.8734 (t0) REVERT: LA 60 ASP cc_start: 0.9147 (t70) cc_final: 0.8586 (t0) REVERT: MA 55 GLU cc_start: 0.9548 (tp30) cc_final: 0.9134 (tp30) REVERT: MA 60 ASP cc_start: 0.8944 (t70) cc_final: 0.8536 (t0) REVERT: NA 60 ASP cc_start: 0.9047 (t0) cc_final: 0.8688 (t0) REVERT: PA 60 ASP cc_start: 0.9108 (t0) cc_final: 0.8833 (t0) REVERT: TA 37 LYS cc_start: 0.9521 (OUTLIER) cc_final: 0.9196 (tttm) REVERT: EA 60 ASP cc_start: 0.9008 (t70) cc_final: 0.8690 (t0) REVERT: HB 124 ARG cc_start: 0.8882 (ttt-90) cc_final: 0.8651 (ttt-90) REVERT: JB 99 GLU cc_start: 0.8776 (mt-10) cc_final: 0.8488 (mt-10) REVERT: QB 127 GLU cc_start: 0.9247 (mm-30) cc_final: 0.9009 (mp0) REVERT: TB 127 GLU cc_start: 0.9245 (mp0) cc_final: 0.8859 (mp0) outliers start: 43 outliers final: 35 residues processed: 515 average time/residue: 0.3352 time to fit residues: 272.0324 Evaluate side-chains 522 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 486 time to evaluate : 2.606 ------------------------------------------------------------------------------- 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 59 LEU Chi-restraints excluded: chain KA residue 69 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 11 ILE Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain QA residue 56 THR Chi-restraints excluded: chain QA residue 73 ASN Chi-restraints excluded: chain RA residue 56 THR Chi-restraints excluded: chain SA residue 56 THR Chi-restraints excluded: chain TA residue 37 LYS Chi-restraints excluded: chain TA residue 56 THR Chi-restraints excluded: chain UA residue 56 THR Chi-restraints excluded: chain VA residue 49 SER Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain IB residue 136 VAL Chi-restraints excluded: chain JB residue 110 SER 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 PB residue 147 SER Chi-restraints excluded: chain RB residue 123 THR Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain SB residue 147 SER Chi-restraints excluded: chain TB residue 147 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 154 optimal weight: 6.9990 chunk 277 optimal weight: 5.9990 chunk 148 optimal weight: 0.9980 chunk 124 optimal weight: 1.9990 chunk 134 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 90 optimal weight: 5.9990 chunk 176 optimal weight: 0.0470 chunk 32 optimal weight: 0.9990 chunk 205 optimal weight: 2.9990 chunk 274 optimal weight: 9.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- 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 = 0.2732 r_free = 0.2732 target = 0.052386 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.2387 r_free = 0.2387 target = 0.039935 restraints weight = 55293.960| |-----------------------------------------------------------------------------| r_work (start): 0.2385 rms_B_bonded: 2.23 r_work: 0.2263 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.2137 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.2137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9326 moved from start: 0.1388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 22572 Z= 0.130 Angle : 0.471 9.234 30800 Z= 0.254 Chirality : 0.039 0.154 3916 Planarity : 0.003 0.050 3784 Dihedral : 4.370 37.269 3146 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.96 % Favored : 97.00 % Rotamer: Outliers : 1.81 % Allowed : 12.04 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.88 (0.15), residues: 2970 helix: 2.12 (0.16), residues: 1056 sheet: 0.10 (0.19), residues: 660 loop : -0.43 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPAB 122 PHE 0.003 0.000 PHEEB 140 TYR 0.007 0.001 TYRIA 34 ARG 0.001 0.000 ARGDB 124 Details of bonding type rmsd hydrogen bonds : bond 0.03448 ( 1110) hydrogen bonds : angle 3.84466 ( 3102) SS BOND : bond 0.00106 ( 44) SS BOND : angle 0.67595 ( 88) covalent geometry : bond 0.00301 (22528) covalent geometry : angle 0.46984 (30712) *********************** 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 549 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 506 time to evaluate : 3.304 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9027 (t70) cc_final: 0.8713 (t0) REVERT: LA 60 ASP cc_start: 0.9125 (t70) cc_final: 0.8585 (t0) REVERT: MA 55 GLU cc_start: 0.9547 (tp30) cc_final: 0.9103 (tp30) REVERT: MA 60 ASP cc_start: 0.8949 (t70) cc_final: 0.8538 (t0) REVERT: NA 55 GLU cc_start: 0.9551 (tp30) cc_final: 0.9109 (tp30) REVERT: NA 60 ASP cc_start: 0.9038 (t70) cc_final: 0.8667 (t0) REVERT: OA 60 ASP cc_start: 0.9340 (OUTLIER) cc_final: 0.8643 (t0) REVERT: PA 60 ASP cc_start: 0.9110 (t0) cc_final: 0.8819 (t0) REVERT: QA 55 GLU cc_start: 0.9429 (tp30) cc_final: 0.9069 (tp30) REVERT: QA 68 GLU cc_start: 0.9104 (tp30) cc_final: 0.8711 (tp30) REVERT: TA 37 LYS cc_start: 0.9518 (OUTLIER) cc_final: 0.9189 (tttm) REVERT: HB 104 GLN cc_start: 0.8760 (OUTLIER) cc_final: 0.8548 (tp40) REVERT: HB 124 ARG cc_start: 0.8857 (ttt-90) cc_final: 0.8635 (ttt-90) REVERT: IB 109 ASN cc_start: 0.8802 (t0) cc_final: 0.8409 (t0) REVERT: JB 99 GLU cc_start: 0.8758 (mt-10) cc_final: 0.8314 (mt-10) REVERT: QB 127 GLU cc_start: 0.9242 (mm-30) cc_final: 0.9018 (mp0) REVERT: TB 127 GLU cc_start: 0.9248 (mp0) cc_final: 0.8864 (mp0) outliers start: 43 outliers final: 31 residues processed: 533 average time/residue: 0.3178 time to fit residues: 268.0858 Evaluate side-chains 525 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 491 time to evaluate : 2.274 ------------------------------------------------------------------------------- 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 59 LEU Chi-restraints excluded: chain KA residue 69 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain MA residue 11 ILE Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain QA residue 56 THR Chi-restraints excluded: chain TA residue 37 LYS Chi-restraints excluded: chain VA residue 49 SER Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain GB residue 121 THR Chi-restraints excluded: chain HB residue 104 GLN Chi-restraints excluded: chain IB residue 136 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 PB residue 147 SER Chi-restraints excluded: chain QB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain SB residue 123 THR Chi-restraints excluded: chain SB residue 147 SER Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain VB residue 83 VAL Chi-restraints excluded: chain BB residue 147 SER Chi-restraints excluded: chain CB residue 83 VAL Chi-restraints excluded: chain DB 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 112 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 222 optimal weight: 8.9990 chunk 101 optimal weight: 0.6980 chunk 49 optimal weight: 0.5980 chunk 18 optimal weight: 0.0010 chunk 75 optimal weight: 0.8980 chunk 166 optimal weight: 0.4980 chunk 216 optimal weight: 8.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.2790 r_free = 0.2790 target = 0.054491 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2455 r_free = 0.2455 target = 0.042147 restraints weight = 55111.283| |-----------------------------------------------------------------------------| r_work (start): 0.2452 rms_B_bonded: 2.24 r_work: 0.2332 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2207 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.2207 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9289 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 22572 Z= 0.086 Angle : 0.441 8.366 30800 Z= 0.237 Chirality : 0.038 0.160 3916 Planarity : 0.003 0.046 3784 Dihedral : 4.048 35.838 3146 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.69 % Favored : 97.27 % Rotamer: Outliers : 1.47 % Allowed : 12.63 % Favored : 85.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.15), residues: 2970 helix: 2.24 (0.16), residues: 1056 sheet: 0.16 (0.19), residues: 660 loop : -0.34 (0.16), residues: 1254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRPQB 122 PHE 0.002 0.000 PHEOB 140 TYR 0.011 0.001 TYRIA 34 ARG 0.001 0.000 ARGDA 42 Details of bonding type rmsd hydrogen bonds : bond 0.03017 ( 1110) hydrogen bonds : angle 3.60130 ( 3102) SS BOND : bond 0.00088 ( 44) SS BOND : angle 0.48977 ( 88) covalent geometry : bond 0.00184 (22528) covalent geometry : angle 0.44067 (30712) *********************** 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 589 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 554 time to evaluate : 2.649 Fit side-chains REVERT: GA 60 ASP cc_start: 0.8980 (t70) cc_final: 0.8670 (t0) REVERT: JA 51 LYS cc_start: 0.9296 (mttp) cc_final: 0.9081 (mtmm) REVERT: KA 60 ASP cc_start: 0.7887 (t0) cc_final: 0.7667 (t0) REVERT: KA 62 LYS cc_start: 0.9470 (mtpp) cc_final: 0.9252 (mtpp) REVERT: LA 60 ASP cc_start: 0.9162 (t70) cc_final: 0.8625 (t0) REVERT: MA 55 GLU cc_start: 0.9545 (tp30) cc_final: 0.9059 (tp30) REVERT: MA 60 ASP cc_start: 0.8946 (t70) cc_final: 0.8532 (t0) REVERT: NA 55 GLU cc_start: 0.9587 (tp30) cc_final: 0.9255 (tp30) REVERT: NA 60 ASP cc_start: 0.9055 (t70) cc_final: 0.8645 (t0) REVERT: OA 60 ASP cc_start: 0.9322 (OUTLIER) cc_final: 0.8596 (t0) REVERT: PA 60 ASP cc_start: 0.9103 (t70) cc_final: 0.8784 (t0) REVERT: QA 55 GLU cc_start: 0.9503 (tp30) cc_final: 0.9155 (tp30) REVERT: QA 68 GLU cc_start: 0.9092 (tp30) cc_final: 0.8729 (tp30) REVERT: SA 55 GLU cc_start: 0.9356 (tp30) cc_final: 0.9056 (tp30) REVERT: TA 68 GLU cc_start: 0.9306 (tp30) cc_final: 0.8942 (tp30) REVERT: IB 109 ASN cc_start: 0.8743 (t0) cc_final: 0.8381 (t0) REVERT: IB 127 GLU cc_start: 0.8835 (pm20) cc_final: 0.8619 (pm20) REVERT: JB 99 GLU cc_start: 0.8798 (mt-10) cc_final: 0.8475 (mt-10) REVERT: TB 127 GLU cc_start: 0.9182 (mp0) cc_final: 0.8803 (mp0) REVERT: EB 99 GLU cc_start: 0.8994 (pt0) cc_final: 0.8470 (pm20) outliers start: 35 outliers final: 22 residues processed: 576 average time/residue: 0.3110 time to fit residues: 282.9141 Evaluate side-chains 549 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 526 time to evaluate : 2.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain IA residue 59 LEU Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain VA residue 9 THR Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain IB residue 136 VAL Chi-restraints excluded: chain JB residue 83 VAL Chi-restraints excluded: chain KB residue 83 VAL Chi-restraints excluded: chain MB residue 83 VAL Chi-restraints excluded: chain OB residue 83 VAL Chi-restraints excluded: chain QB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain TB residue 147 SER 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 DB residue 83 VAL Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 150 optimal weight: 6.9990 chunk 152 optimal weight: 0.9990 chunk 105 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 chunk 284 optimal weight: 3.9990 chunk 173 optimal weight: 2.9990 chunk 147 optimal weight: 7.9990 chunk 254 optimal weight: 3.9990 chunk 218 optimal weight: 4.9990 chunk 79 optimal weight: 0.9990 chunk 283 optimal weight: 5.9990 overall best weight: 2.1990 ------------------------------------------------------------------------------- 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 = 0.2716 r_free = 0.2716 target = 0.051648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2363 r_free = 0.2363 target = 0.039053 restraints weight = 55945.935| |-----------------------------------------------------------------------------| r_work (start): 0.2361 rms_B_bonded: 2.27 r_work: 0.2238 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2112 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9351 moved from start: 0.1479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 22572 Z= 0.186 Angle : 0.520 8.408 30800 Z= 0.278 Chirality : 0.041 0.191 3916 Planarity : 0.003 0.050 3784 Dihedral : 4.355 37.236 3146 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 3.27 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.86 % Favored : 97.10 % Rotamer: Outliers : 1.52 % Allowed : 13.22 % Favored : 85.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.15), residues: 2970 helix: 2.30 (0.16), residues: 1034 sheet: 0.13 (0.19), residues: 660 loop : -0.44 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPAB 122 PHE 0.004 0.001 PHEPB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGHB 124 Details of bonding type rmsd hydrogen bonds : bond 0.03757 ( 1110) hydrogen bonds : angle 3.92097 ( 3102) SS BOND : bond 0.00104 ( 44) SS BOND : angle 0.85690 ( 88) covalent geometry : bond 0.00444 (22528) covalent geometry : angle 0.51834 (30712) *********************** 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 530 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 494 time to evaluate : 2.384 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9026 (t70) cc_final: 0.8708 (t0) REVERT: HA 55 GLU cc_start: 0.9161 (tp30) cc_final: 0.8909 (tp30) REVERT: JA 51 LYS cc_start: 0.9413 (mttp) cc_final: 0.9029 (mttm) REVERT: KA 60 ASP cc_start: 0.7981 (t0) cc_final: 0.7780 (t0) REVERT: KA 62 LYS cc_start: 0.9481 (mtpp) cc_final: 0.9256 (mtpp) REVERT: LA 55 GLU cc_start: 0.9496 (tp30) cc_final: 0.9276 (tp30) REVERT: LA 60 ASP cc_start: 0.9158 (t70) cc_final: 0.8581 (t0) REVERT: MA 55 GLU cc_start: 0.9556 (tp30) cc_final: 0.9084 (tp30) REVERT: MA 60 ASP cc_start: 0.8980 (t70) cc_final: 0.8561 (t0) REVERT: NA 60 ASP cc_start: 0.9073 (t70) cc_final: 0.8660 (t0) REVERT: OA 60 ASP cc_start: 0.9355 (OUTLIER) cc_final: 0.8652 (t0) REVERT: PA 60 ASP cc_start: 0.9114 (t70) cc_final: 0.8802 (t0) REVERT: QA 68 GLU cc_start: 0.9132 (tp30) cc_final: 0.8756 (tp30) REVERT: TA 37 LYS cc_start: 0.9546 (OUTLIER) cc_final: 0.9228 (tttm) REVERT: EA 60 ASP cc_start: 0.8939 (t70) cc_final: 0.8721 (t0) REVERT: IB 109 ASN cc_start: 0.8885 (t0) cc_final: 0.8502 (t0) REVERT: JB 99 GLU cc_start: 0.8756 (mt-10) cc_final: 0.8466 (mt-10) REVERT: TB 127 GLU cc_start: 0.9247 (mp0) cc_final: 0.8865 (mp0) outliers start: 36 outliers final: 29 residues processed: 517 average time/residue: 0.3284 time to fit residues: 266.8558 Evaluate side-chains 522 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 491 time to evaluate : 2.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain TA residue 37 LYS Chi-restraints excluded: chain UA residue 56 THR Chi-restraints excluded: chain VA residue 9 THR Chi-restraints excluded: chain VA residue 49 SER Chi-restraints excluded: chain EA residue 11 ILE Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain IB residue 136 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 PB residue 147 SER Chi-restraints excluded: chain QB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain TB residue 147 SER Chi-restraints excluded: chain UB residue 83 VAL Chi-restraints excluded: chain VB residue 83 VAL Chi-restraints excluded: chain AB residue 121 THR 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 DB residue 83 VAL Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain FB residue 121 THR Chi-restraints excluded: chain FB residue 147 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 286 random chunks: chunk 202 optimal weight: 0.1980 chunk 226 optimal weight: 7.9990 chunk 260 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 88 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 112 optimal weight: 0.6980 chunk 117 optimal weight: 0.9990 chunk 87 optimal weight: 0.2980 chunk 6 optimal weight: 3.9990 chunk 97 optimal weight: 0.0040 overall best weight: 0.3792 ------------------------------------------------------------------------------- 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 = 0.2802 r_free = 0.2802 target = 0.055351 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2469 r_free = 0.2469 target = 0.042836 restraints weight = 54545.308| |-----------------------------------------------------------------------------| r_work (start): 0.2465 rms_B_bonded: 2.34 r_work: 0.2344 rms_B_bonded: 2.65 restraints_weight: 0.5000 r_work: 0.2217 rms_B_bonded: 4.36 restraints_weight: 0.2500 r_work (final): 0.2217 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9277 moved from start: 0.1416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 22572 Z= 0.086 Angle : 0.455 7.621 30800 Z= 0.243 Chirality : 0.038 0.171 3916 Planarity : 0.003 0.046 3784 Dihedral : 4.004 35.411 3146 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 4.25 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.39 % Favored : 97.58 % Rotamer: Outliers : 1.18 % Allowed : 14.06 % Favored : 84.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.03 (0.15), residues: 2970 helix: 2.25 (0.16), residues: 1056 sheet: 0.21 (0.21), residues: 572 loop : -0.34 (0.16), residues: 1342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRPQB 122 PHE 0.003 0.001 PHEJB 107 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGBA 42 Details of bonding type rmsd hydrogen bonds : bond 0.02982 ( 1110) hydrogen bonds : angle 3.57273 ( 3102) SS BOND : bond 0.00095 ( 44) SS BOND : angle 0.51713 ( 88) covalent geometry : bond 0.00181 (22528) covalent geometry : angle 0.45479 (30712) *********************** 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 580 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 552 time to evaluate : 2.616 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9001 (t70) cc_final: 0.8690 (t0) REVERT: JA 51 LYS cc_start: 0.9330 (mttp) cc_final: 0.9120 (mtmm) REVERT: KA 60 ASP cc_start: 0.7987 (t0) cc_final: 0.7773 (t0) REVERT: KA 62 LYS cc_start: 0.9457 (mtpp) cc_final: 0.9237 (mtpp) REVERT: LA 60 ASP cc_start: 0.9186 (t70) cc_final: 0.8609 (t0) REVERT: MA 55 GLU cc_start: 0.9558 (tp30) cc_final: 0.9077 (tp30) REVERT: MA 60 ASP cc_start: 0.8973 (t70) cc_final: 0.8548 (t0) REVERT: NA 55 GLU cc_start: 0.9594 (tp30) cc_final: 0.9278 (tp30) REVERT: NA 60 ASP cc_start: 0.9052 (t70) cc_final: 0.8599 (t0) REVERT: OA 60 ASP cc_start: 0.9314 (OUTLIER) cc_final: 0.8687 (t0) REVERT: PA 60 ASP cc_start: 0.9103 (t70) cc_final: 0.8772 (t0) REVERT: QA 55 GLU cc_start: 0.9446 (tp30) cc_final: 0.9166 (tp30) REVERT: QA 68 GLU cc_start: 0.9109 (tp30) cc_final: 0.8750 (tp30) REVERT: SA 55 GLU cc_start: 0.9354 (tp30) cc_final: 0.9086 (tp30) REVERT: TA 68 GLU cc_start: 0.9277 (tp30) cc_final: 0.8762 (tp30) REVERT: IB 109 ASN cc_start: 0.8706 (t0) cc_final: 0.8315 (t0) REVERT: JB 99 GLU cc_start: 0.8791 (mt-10) cc_final: 0.8327 (mt-10) REVERT: RB 127 GLU cc_start: 0.8884 (mp0) cc_final: 0.8565 (mp0) REVERT: TB 127 GLU cc_start: 0.9214 (mp0) cc_final: 0.8845 (mp0) outliers start: 28 outliers final: 24 residues processed: 572 average time/residue: 0.3217 time to fit residues: 293.5199 Evaluate side-chains 559 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 534 time to evaluate : 2.653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain VA residue 9 THR Chi-restraints excluded: chain VA residue 49 SER Chi-restraints excluded: chain EA residue 11 ILE Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain IB residue 136 VAL Chi-restraints excluded: chain JB 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 QB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain TB residue 147 SER 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 DB residue 83 VAL Chi-restraints excluded: chain FB residue 121 THR 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 146 optimal weight: 0.9980 chunk 100 optimal weight: 3.9990 chunk 244 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 148 optimal weight: 5.9990 chunk 163 optimal weight: 2.9990 chunk 250 optimal weight: 6.9990 chunk 227 optimal weight: 2.9990 chunk 142 optimal weight: 3.9990 chunk 125 optimal weight: 0.0670 overall best weight: 2.0124 ------------------------------------------------------------------------------- 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 = 0.2723 r_free = 0.2723 target = 0.052451 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2371 r_free = 0.2371 target = 0.039778 restraints weight = 55393.944| |-----------------------------------------------------------------------------| r_work (start): 0.2368 rms_B_bonded: 2.32 r_work: 0.2244 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2117 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2117 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9333 moved from start: 0.1520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 22572 Z= 0.170 Angle : 0.515 7.965 30800 Z= 0.276 Chirality : 0.040 0.174 3916 Planarity : 0.003 0.049 3784 Dihedral : 4.293 37.009 3146 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 3.59 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.90 % Favored : 97.07 % Rotamer: Outliers : 1.18 % Allowed : 13.85 % Favored : 84.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.98 (0.15), residues: 2970 helix: 2.30 (0.16), residues: 1034 sheet: 0.15 (0.19), residues: 660 loop : -0.43 (0.16), residues: 1276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRPBB 122 PHE 0.004 0.001 PHEEB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGHB 124 Details of bonding type rmsd hydrogen bonds : bond 0.03706 ( 1110) hydrogen bonds : angle 3.87713 ( 3102) SS BOND : bond 0.00128 ( 44) SS BOND : angle 0.85967 ( 88) covalent geometry : bond 0.00401 (22528) covalent geometry : angle 0.51376 (30712) ********************** 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 523 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 495 time to evaluate : 2.328 Fit side-chains REVERT: GA 60 ASP cc_start: 0.9030 (t70) cc_final: 0.8703 (t0) REVERT: HA 55 GLU cc_start: 0.9170 (tp30) cc_final: 0.8896 (tp30) REVERT: JA 51 LYS cc_start: 0.9393 (mttp) cc_final: 0.9186 (mtmm) REVERT: KA 60 ASP cc_start: 0.7909 (t0) cc_final: 0.7702 (t0) REVERT: KA 62 LYS cc_start: 0.9468 (mtpp) cc_final: 0.9235 (mtpp) REVERT: LA 55 GLU cc_start: 0.9531 (tp30) cc_final: 0.9306 (tp30) REVERT: LA 60 ASP cc_start: 0.9196 (t70) cc_final: 0.8635 (t0) REVERT: MA 55 GLU cc_start: 0.9575 (tp30) cc_final: 0.9109 (tp30) REVERT: MA 60 ASP cc_start: 0.9011 (t70) cc_final: 0.8579 (t0) REVERT: NA 60 ASP cc_start: 0.9093 (t70) cc_final: 0.8659 (t0) REVERT: OA 60 ASP cc_start: 0.9329 (OUTLIER) cc_final: 0.8649 (t0) REVERT: PA 60 ASP cc_start: 0.9106 (t70) cc_final: 0.8767 (t0) REVERT: QA 55 GLU cc_start: 0.9445 (tp30) cc_final: 0.9085 (tp30) REVERT: QA 60 ASP cc_start: 0.8987 (t70) cc_final: 0.8732 (t0) REVERT: QA 68 GLU cc_start: 0.9122 (tp30) cc_final: 0.8734 (tp30) REVERT: IB 109 ASN cc_start: 0.8874 (t0) cc_final: 0.8488 (t0) REVERT: JB 99 GLU cc_start: 0.8735 (mt-10) cc_final: 0.8407 (mt-10) REVERT: RB 127 GLU cc_start: 0.9013 (mp0) cc_final: 0.8673 (mp0) REVERT: TB 127 GLU cc_start: 0.9244 (mp0) cc_final: 0.8840 (mp0) REVERT: BB 79 SER cc_start: 0.8568 (t) cc_final: 0.8217 (p) outliers start: 28 outliers final: 25 residues processed: 513 average time/residue: 0.3156 time to fit residues: 255.1284 Evaluate side-chains 519 residues out of total 2376 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 493 time to evaluate : 2.506 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain HA residue 11 ILE Chi-restraints excluded: chain IA residue 49 SER Chi-restraints excluded: chain LA residue 77 LEU Chi-restraints excluded: chain OA residue 60 ASP Chi-restraints excluded: chain PA residue 52 THR Chi-restraints excluded: chain RA residue 49 SER Chi-restraints excluded: chain GB residue 83 VAL Chi-restraints excluded: chain IB residue 136 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 QB residue 83 VAL Chi-restraints excluded: chain SB residue 83 VAL Chi-restraints excluded: chain TB residue 147 SER 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 DB residue 83 VAL Chi-restraints excluded: chain EB residue 83 VAL Chi-restraints excluded: chain FB residue 121 THR 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 173 optimal weight: 5.9990 chunk 126 optimal weight: 4.9990 chunk 253 optimal weight: 6.9990 chunk 170 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 chunk 160 optimal weight: 10.0000 chunk 151 optimal weight: 0.9980 chunk 245 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 168 optimal weight: 0.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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 = 0.2740 r_free = 0.2740 target = 0.053165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2396 r_free = 0.2396 target = 0.040590 restraints weight = 54736.571| |-----------------------------------------------------------------------------| r_work (start): 0.2392 rms_B_bonded: 2.30 r_work: 0.2269 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2142 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9320 moved from start: 0.1474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 22572 Z= 0.130 Angle : 0.491 7.924 30800 Z= 0.264 Chirality : 0.039 0.164 3916 Planarity : 0.003 0.048 3784 Dihedral : 4.249 36.525 3146 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 3.61 Ramachandran Plot: Outliers : 0.03 % Allowed : 2.76 % Favored : 97.21 % Rotamer: Outliers : 1.14 % Allowed : 14.48 % Favored : 84.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.03 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.15), residues: 2970 helix: 2.10 (0.16), residues: 1056 sheet: 0.14 (0.20), residues: 616 loop : -0.40 (0.16), residues: 1298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRPBB 122 PHE 0.003 0.001 PHEPB 140 TYR 0.010 0.001 TYRIA 34 ARG 0.002 0.000 ARGHB 124 Details of bonding type rmsd hydrogen bonds : bond 0.03450 ( 1110) hydrogen bonds : angle 3.79356 ( 3102) SS BOND : bond 0.00121 ( 44) SS BOND : angle 0.77949 ( 88) covalent geometry : bond 0.00303 (22528) covalent geometry : angle 0.49002 (30712) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11997.62 seconds wall clock time: 208 minutes 5.14 seconds (12485.14 seconds total)