Starting phenix.real_space_refine on Thu Jul 2 05:02:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7wp6_32676/07_2026/7wp6_32676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp6_32676/07_2026/7wp6_32676.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.81 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7wp6_32676/07_2026/7wp6_32676.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7wp6_32676/07_2026/7wp6_32676.cif" model { file = "/net/cci-nas-00/data/ceres_data/7wp6_32676/07_2026/7wp6_32676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp6_32676/07_2026/7wp6_32676.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7wp6_32676/07_2026/7wp6_32676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp6_32676/07_2026/7wp6_32676.map" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 30 5.16 5 C 4278 2.51 5 N 1111 2.21 5 O 1329 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 6748 Number of models: 1 Model: "" Number of chains: 9 Chain: "B" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 115} Chain: "C" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 805 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 4, 'TRANS': 98} Chain: "D" Number of atoms: 919 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 919 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "F" Number of atoms: 1462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1462 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 9, 'TRANS': 173} Chain: "H" Number of atoms: 930 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 930 Classifications: {'peptide': 118} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 113} Chain: "I" Number of atoms: 875 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 875 Classifications: {'peptide': 113} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 107} Chain: "L" Number of atoms: 791 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 791 Classifications: {'peptide': 106} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 8, 'TRANS': 97} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Chain: "L" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 1.15, per 1000 atoms: 0.17 Number of scatterers: 6748 At special positions: 0 Unit cell: (77.022, 109.698, 126.036, 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 30 16.00 O 1329 8.00 N 1111 7.00 C 4278 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " distance=2.03 Simple disulfide: pdb=" SG CYS C 23 " - pdb=" SG CYS C 88 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 96 " distance=2.03 Simple disulfide: pdb=" SG CYS F 379 " - pdb=" SG CYS F 432 " distance=2.72 Simple disulfide: pdb=" SG CYS F 480 " - pdb=" SG CYS F 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.02 Simple disulfide: pdb=" SG CYS I 23 " - pdb=" SG CYS I 94 " distance=2.04 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN F 343 " " NAG L 201 " - " ASN L 26 " Time building additional restraints: 0.44 Conformation dependent library (CDL) restraints added in 267.0 milliseconds 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1568 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 18 sheets defined 1.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'F' and resid 405 through 410 removed outlier: 4.893A pdb=" N ARG F 408 " --> pdb=" O ASP F 405 " (cutoff:3.500A) removed outlier: 3.771A pdb=" N ILE F 410 " --> pdb=" O VAL F 407 " (cutoff:3.500A) Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'I' and resid 85 through 89 removed outlier: 3.826A pdb=" N LEU I 89 " --> pdb=" O ALA I 86 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 3 through 5 removed outlier: 3.748A pdb=" N GLN B 3 " --> pdb=" O SER B 25 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N SER B 25 " --> pdb=" O GLN B 3 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 10 through 12 removed outlier: 3.687A pdb=" N THR B 117 " --> pdb=" O GLU B 10 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N VAL B 12 " --> pdb=" O THR B 117 " (cutoff:3.500A) removed outlier: 6.799A pdb=" N MET B 34 " --> pdb=" O GLY B 50 " (cutoff:3.500A) removed outlier: 4.776A pdb=" N GLY B 50 " --> pdb=" O MET B 34 " (cutoff:3.500A) removed outlier: 6.763A pdb=" N TRP B 36 " --> pdb=" O ILE B 48 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N LYS B 38 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 4.392A pdb=" N GLU B 46 " --> pdb=" O LYS B 38 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N ILE B 59 " --> pdb=" O GLY B 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.108A pdb=" N LEU C 11 " --> pdb=" O GLU C 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 19 through 24 removed outlier: 3.617A pdb=" N THR C 63 " --> pdb=" O THR C 74 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 53 through 54 removed outlier: 3.618A pdb=" N THR C 53 " --> pdb=" O SER C 49 " (cutoff:3.500A) removed outlier: 5.738A pdb=" N LEU C 46 " --> pdb=" O GLN C 37 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N GLN C 37 " --> pdb=" O LEU C 46 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N GLN C 38 " --> pdb=" O ASP C 85 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ASP C 85 " --> pdb=" O GLN C 38 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.711A pdb=" N THR D 117 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 6.940A pdb=" N MET D 34 " --> pdb=" O ALA D 50 " (cutoff:3.500A) removed outlier: 4.606A pdb=" N ALA D 50 " --> pdb=" O MET D 34 " (cutoff:3.500A) removed outlier: 7.082A pdb=" N TRP D 36 " --> pdb=" O ILE D 48 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 10 through 11 removed outlier: 3.711A pdb=" N THR D 117 " --> pdb=" O GLU D 10 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 22 through 23 removed outlier: 3.722A pdb=" N THR D 78 " --> pdb=" O ASP D 73 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'F' and resid 354 through 358 removed outlier: 3.507A pdb=" N ASN F 354 " --> pdb=" O SER F 399 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N VAL F 395 " --> pdb=" O ILE F 358 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N ASN F 394 " --> pdb=" O GLU F 516 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'F' and resid 452 through 454 Processing sheet with id=AB2, first strand: chain 'H' and resid 5 through 6 removed outlier: 3.901A pdb=" N THR H 78 " --> pdb=" O ASP H 73 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.711A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE H 95 " --> pdb=" O VAL H 37 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL H 37 " --> pdb=" O PHE H 95 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.479A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.744A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.711A pdb=" N THR H 112 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N PHE H 107 " --> pdb=" O GLY H 98 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'I' and resid 4 through 6 removed outlier: 3.813A pdb=" N SER I 5 " --> pdb=" O LYS I 24 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N CYS I 23 " --> pdb=" O PHE I 77 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP I 76 " --> pdb=" O SER I 73 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'I' and resid 30 through 31 removed outlier: 3.506A pdb=" N LYS I 36 " --> pdb=" O TYR I 31 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'I' and resid 51 through 52 removed outlier: 4.011A pdb=" N CYS I 94 " --> pdb=" O GLY I 105 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N GLY I 105 " --> pdb=" O CYS I 94 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'L' and resid 4 through 5 removed outlier: 3.772A pdb=" N SER L 69 " --> pdb=" O SER L 66 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N SER L 66 " --> pdb=" O SER L 69 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.683A pdb=" N TRP L 34 " --> pdb=" O TRP L 46 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N TRP L 46 " --> pdb=" O TRP L 34 " (cutoff:3.500A) 163 hydrogen bonds defined for protein. 402 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.63 Time building geometry restraints manager: 0.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2091 1.34 - 1.46: 1794 1.46 - 1.58: 2997 1.58 - 1.70: 0 1.70 - 1.82: 40 Bond restraints: 6922 Sorted by residual: bond pdb=" C TYR H 52 " pdb=" N PRO H 53 " ideal model delta sigma weight residual 1.337 1.307 0.030 1.06e-02 8.90e+03 7.91e+00 bond pdb=" CA CYS H 22 " pdb=" CB CYS H 22 " ideal model delta sigma weight residual 1.524 1.486 0.037 1.62e-02 3.81e+03 5.34e+00 bond pdb=" CA ALA L 25 " pdb=" C ALA L 25 " ideal model delta sigma weight residual 1.522 1.496 0.026 1.23e-02 6.61e+03 4.49e+00 bond pdb=" C VAL I 64 " pdb=" N PRO I 65 " ideal model delta sigma weight residual 1.331 1.356 -0.025 1.20e-02 6.94e+03 4.41e+00 bond pdb=" CA ALA F 344 " pdb=" C ALA F 344 " ideal model delta sigma weight residual 1.526 1.497 0.028 1.36e-02 5.41e+03 4.28e+00 ... (remaining 6917 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.15: 9227 3.15 - 6.30: 149 6.30 - 9.44: 18 9.44 - 12.59: 3 12.59 - 15.74: 1 Bond angle restraints: 9398 Sorted by residual: angle pdb=" N SER L 27 " pdb=" CA SER L 27 " pdb=" C SER L 27 " ideal model delta sigma weight residual 110.80 120.85 -10.05 2.13e+00 2.20e-01 2.22e+01 angle pdb=" C GLN I 48 " pdb=" N SER I 49 " pdb=" CA SER I 49 " ideal model delta sigma weight residual 121.27 137.01 -15.74 3.40e+00 8.65e-02 2.14e+01 angle pdb=" C TYR L 48 " pdb=" N ALA L 49 " pdb=" CA ALA L 49 " ideal model delta sigma weight residual 121.19 128.35 -7.16 1.59e+00 3.96e-01 2.03e+01 angle pdb=" N PHE I 100 " pdb=" CA PHE I 100 " pdb=" C PHE I 100 " ideal model delta sigma weight residual 109.81 119.75 -9.94 2.21e+00 2.05e-01 2.02e+01 angle pdb=" C SER B 40 " pdb=" N HIS B 41 " pdb=" CA HIS B 41 " ideal model delta sigma weight residual 122.36 128.23 -5.87 1.42e+00 4.96e-01 1.71e+01 ... (remaining 9393 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.61: 3485 16.61 - 33.21: 448 33.21 - 49.82: 73 49.82 - 66.43: 12 66.43 - 83.03: 9 Dihedral angle restraints: 4027 sinusoidal: 1545 harmonic: 2482 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 169.57 -76.57 1 1.00e+01 1.00e-02 7.37e+01 dihedral pdb=" CA TRP C 50 " pdb=" C TRP C 50 " pdb=" N ALA C 51 " pdb=" CA ALA C 51 " ideal model delta harmonic sigma weight residual -180.00 -144.27 -35.73 0 5.00e+00 4.00e-02 5.11e+01 dihedral pdb=" CB CYS F 480 " pdb=" SG CYS F 480 " pdb=" SG CYS F 488 " pdb=" CB CYS F 488 " ideal model delta sinusoidal sigma weight residual -86.00 -133.21 47.21 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 4024 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.079: 859 0.079 - 0.159: 126 0.159 - 0.238: 14 0.238 - 0.318: 3 0.318 - 0.397: 4 Chirality restraints: 1006 Sorted by residual: chirality pdb=" CA SER L 27 " pdb=" N SER L 27 " pdb=" C SER L 27 " pdb=" CB SER L 27 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.94e+00 chirality pdb=" CB ILE H 51 " pdb=" CA ILE H 51 " pdb=" CG1 ILE H 51 " pdb=" CG2 ILE H 51 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.59e+00 chirality pdb=" CB THR C 102 " pdb=" CA THR C 102 " pdb=" OG1 THR C 102 " pdb=" CG2 THR C 102 " both_signs ideal model delta sigma weight residual False 2.55 2.21 0.34 2.00e-01 2.50e+01 2.89e+00 ... (remaining 1003 not shown) Planarity restraints: 1201 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG L 201 " 0.328 2.00e-02 2.50e+03 2.84e-01 1.01e+03 pdb=" C7 NAG L 201 " -0.076 2.00e-02 2.50e+03 pdb=" C8 NAG L 201 " 0.046 2.00e-02 2.50e+03 pdb=" N2 NAG L 201 " -0.499 2.00e-02 2.50e+03 pdb=" O7 NAG L 201 " 0.200 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 1 " 0.240 2.00e-02 2.50e+03 2.05e-01 5.26e+02 pdb=" C7 NAG A 1 " -0.052 2.00e-02 2.50e+03 pdb=" C8 NAG A 1 " -0.030 2.00e-02 2.50e+03 pdb=" N2 NAG A 1 " -0.341 2.00e-02 2.50e+03 pdb=" O7 NAG A 1 " 0.182 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C2 NAG A 2 " -0.122 2.00e-02 2.50e+03 1.01e-01 1.27e+02 pdb=" C7 NAG A 2 " 0.032 2.00e-02 2.50e+03 pdb=" C8 NAG A 2 " -0.091 2.00e-02 2.50e+03 pdb=" N2 NAG A 2 " 0.162 2.00e-02 2.50e+03 pdb=" O7 NAG A 2 " 0.018 2.00e-02 2.50e+03 ... (remaining 1198 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1243 2.76 - 3.29: 5754 3.29 - 3.83: 10868 3.83 - 4.36: 11903 4.36 - 4.90: 21382 Nonbonded interactions: 51150 Sorted by model distance: nonbonded pdb=" O ASP C 30 " pdb=" OD1 ASP C 30 " model vdw 2.224 3.040 nonbonded pdb=" OG1 THR F 478 " pdb=" O TYR I 98 " model vdw 2.254 3.040 nonbonded pdb=" O SER F 438 " pdb=" OG SER F 438 " model vdw 2.276 3.040 nonbonded pdb=" OD1 ASP F 442 " pdb=" OH TYR F 451 " model vdw 2.318 3.040 nonbonded pdb=" O THR D 114 " pdb=" OG1 THR D 114 " model vdw 2.321 3.040 ... (remaining 51145 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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 group one per residue 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: 5.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.120 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.640 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:0.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 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 : 0.011 0.684 6932 Z= 0.547 Angle : 1.138 32.640 9421 Z= 0.621 Chirality : 0.062 0.397 1006 Planarity : 0.013 0.284 1199 Dihedral : 14.930 83.035 2438 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.45 % Favored : 90.44 % Rotamer: Outliers : 0.69 % Allowed : 12.07 % Favored : 87.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -3.82 (0.24), residues: 847 helix: -5.32 (0.38), residues: 8 sheet: -1.64 (0.29), residues: 290 loop : -3.20 (0.21), residues: 549 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG F 355 TYR 0.032 0.003 TYR I 55 PHE 0.029 0.003 PHE I 100 TRP 0.027 0.003 TRP I 56 HIS 0.006 0.003 HIS H 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00768 / 0.36 ( 6922) covalent geometry : angle 1.06603 / 0.59 ( 9398) SS BOND : bond 0.25876 / 12.94 ( 7) SS BOND : angle 9.81092 / 6.05 ( 14) hydrogen bonds : bond 0.28652 / 18.46 ( 154) hydrogen bonds : angle 11.18493 / 7.61 ( 402) link_BETA1-4 : bond 0.01095 / 0.58 ( 1) link_BETA1-4 : angle 6.88447 / 3.68 ( 3) link_NAG-ASN : bond 0.00701 / 0.34 ( 2) link_NAG-ASN : angle 2.08832 / 1.21 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 247 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 242 time to evaluate : 0.194 Fit side-chains REVERT: B 10 GLU cc_start: 0.8777 (mm-30) cc_final: 0.8433 (mp0) REVERT: C 27 GLN cc_start: 0.7769 (mp10) cc_final: 0.7190 (mp10) REVERT: C 54 ARG cc_start: 0.8072 (ptp90) cc_final: 0.7803 (ptp90) REVERT: D 83 LEU cc_start: 0.9041 (mt) cc_final: 0.8733 (mp) REVERT: F 414 GLN cc_start: 0.7616 (tt0) cc_final: 0.7164 (mp10) REVERT: F 465 GLU cc_start: 0.8573 (tp30) cc_final: 0.8228 (tp30) REVERT: H 73 ASP cc_start: 0.7839 (m-30) cc_final: 0.7029 (p0) outliers start: 5 outliers final: 4 residues processed: 245 average time/residue: 0.0790 time to fit residues: 25.0304 Evaluate side-chains 194 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 190 time to evaluate : 0.162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain I residue 42 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 49 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0770 chunk 51 optimal weight: 9.9990 chunk 38 optimal weight: 0.5980 chunk 61 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 74 optimal weight: 4.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN C 79 GLN C 90 GLN D 62 GLN F 487 ASN F 493 GLN I 96 GLN L 52 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.141355 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.108406 restraints weight = 12451.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.112108 restraints weight = 7858.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.114612 restraints weight = 5869.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 42)----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.116363 restraints weight = 4857.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.3551 r_free = 0.3551 target = 0.117520 restraints weight = 4263.968| |-----------------------------------------------------------------------------| r_work (final): 0.3551 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7821 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6932 Z= 0.148 Angle : 0.693 12.368 9421 Z= 0.352 Chirality : 0.045 0.216 1006 Planarity : 0.005 0.059 1199 Dihedral : 6.229 40.990 952 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.10 % Rotamer: Outliers : 3.43 % Allowed : 21.26 % Favored : 75.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.96 (0.27), residues: 847 helix: -5.22 (0.43), residues: 8 sheet: -0.97 (0.28), residues: 350 loop : -2.80 (0.24), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 61 TYR 0.021 0.002 TYR I 42 PHE 0.025 0.002 PHE I 100 TRP 0.024 0.002 TRP I 56 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00329 / 0.15 ( 6922) covalent geometry : angle 0.68303 / 0.35 ( 9398) SS BOND : bond 0.00526 / 0.17 ( 7) SS BOND : angle 1.56183 / 0.91 ( 14) hydrogen bonds : bond 0.04508 / 2.85 ( 154) hydrogen bonds : angle 7.79254 / 5.36 ( 402) link_BETA1-4 : bond 0.01075 / 0.57 ( 1) link_BETA1-4 : angle 5.13995 / 2.78 ( 3) link_NAG-ASN : bond 0.00210 / 0.11 ( 2) link_NAG-ASN : angle 1.92402 / 1.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 213 time to evaluate : 0.248 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7742 (m-80) cc_final: 0.7381 (m-80) REVERT: B 89 GLU cc_start: 0.7482 (mp0) cc_final: 0.7203 (mp0) REVERT: C 18 ARG cc_start: 0.4530 (OUTLIER) cc_final: 0.3716 (ttp-110) REVERT: C 54 ARG cc_start: 0.7715 (ptp90) cc_final: 0.7500 (ptp90) REVERT: D 60 TYR cc_start: 0.8832 (m-10) cc_final: 0.8454 (m-80) REVERT: D 80 TYR cc_start: 0.7918 (m-80) cc_final: 0.7612 (m-10) REVERT: F 414 GLN cc_start: 0.7344 (tt0) cc_final: 0.7077 (mp10) REVERT: H 38 LYS cc_start: 0.8894 (ttmm) cc_final: 0.8667 (ttmm) REVERT: I 41 TRP cc_start: 0.8562 (m100) cc_final: 0.8246 (m100) REVERT: I 56 TRP cc_start: 0.7148 (m100) cc_final: 0.6122 (m100) REVERT: L 38 LYS cc_start: 0.9174 (tppp) cc_final: 0.8648 (ttpt) outliers start: 25 outliers final: 19 residues processed: 224 average time/residue: 0.0762 time to fit residues: 22.1261 Evaluate side-chains 203 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 18 VAL Chi-restraints excluded: chain B residue 83 LEU Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain C residue 103 LYS Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 113 THR Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 4 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 39 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 12 optimal weight: 7.9990 chunk 0 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 chunk 77 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 25 optimal weight: 0.0050 chunk 63 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 62 optimal weight: 0.6980 overall best weight: 0.7196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3861 r_free = 0.3861 target = 0.140502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.107852 restraints weight = 12373.999| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3472 r_free = 0.3472 target = 0.111565 restraints weight = 7769.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.114013 restraints weight = 5791.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3529 r_free = 0.3529 target = 0.115713 restraints weight = 4788.885| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.116759 restraints weight = 4211.384| |-----------------------------------------------------------------------------| r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 6932 Z= 0.144 Angle : 0.683 13.328 9421 Z= 0.340 Chirality : 0.044 0.191 1006 Planarity : 0.005 0.057 1199 Dihedral : 5.965 42.333 952 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer: Outliers : 5.08 % Allowed : 21.26 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.58 (0.27), residues: 847 helix: -5.18 (0.46), residues: 8 sheet: -0.58 (0.28), residues: 348 loop : -2.64 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 76 TYR 0.022 0.002 TYR I 42 PHE 0.027 0.002 PHE I 77 TRP 0.018 0.001 TRP I 56 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6922) covalent geometry : angle 0.67401 / 0.34 ( 9398) SS BOND : bond 0.00490 / 0.19 ( 7) SS BOND : angle 1.51424 / 0.87 ( 14) hydrogen bonds : bond 0.03818 / 2.40 ( 154) hydrogen bonds : angle 7.00233 / 4.80 ( 402) link_BETA1-4 : bond 0.01111 / 0.58 ( 1) link_BETA1-4 : angle 5.09707 / 2.76 ( 3) link_NAG-ASN : bond 0.00109 / 0.06 ( 2) link_NAG-ASN : angle 1.46284 / 0.85 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 201 time to evaluate : 0.344 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 GLU cc_start: 0.7576 (mp0) cc_final: 0.7231 (mp0) REVERT: C 18 ARG cc_start: 0.4698 (OUTLIER) cc_final: 0.3855 (ttp-110) REVERT: C 54 ARG cc_start: 0.7717 (ptp90) cc_final: 0.7452 (ptp90) REVERT: D 60 TYR cc_start: 0.8889 (m-10) cc_final: 0.8641 (m-80) REVERT: H 38 LYS cc_start: 0.8914 (ttmm) cc_final: 0.8599 (ttmm) REVERT: I 41 TRP cc_start: 0.8501 (m100) cc_final: 0.8246 (m100) REVERT: I 73 SER cc_start: 0.7490 (t) cc_final: 0.7049 (m) REVERT: L 38 LYS cc_start: 0.9189 (tppp) cc_final: 0.8656 (ttpt) outliers start: 37 outliers final: 28 residues processed: 217 average time/residue: 0.0729 time to fit residues: 20.8698 Evaluate side-chains 218 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 189 time to evaluate : 0.170 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain F residue 503 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.8980 chunk 22 optimal weight: 7.9990 chunk 72 optimal weight: 7.9990 chunk 40 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 15 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 41 HIS ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3811 r_free = 0.3811 target = 0.136519 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103917 restraints weight = 12655.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107347 restraints weight = 8150.839| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.109690 restraints weight = 6186.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.111209 restraints weight = 5167.372| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112335 restraints weight = 4591.719| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7929 moved from start: 0.3157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6932 Z= 0.229 Angle : 0.739 13.290 9421 Z= 0.371 Chirality : 0.045 0.224 1006 Planarity : 0.005 0.056 1199 Dihedral : 6.288 52.335 952 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.67 % Favored : 92.21 % Rotamer: Outliers : 7.27 % Allowed : 20.71 % Favored : 72.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.57 (0.28), residues: 847 helix: -5.17 (0.50), residues: 8 sheet: -0.62 (0.28), residues: 344 loop : -2.58 (0.25), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 76 TYR 0.024 0.002 TYR F 380 PHE 0.025 0.002 PHE I 100 TRP 0.021 0.002 TRP I 56 HIS 0.004 0.001 HIS L 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00527 / 0.23 ( 6922) covalent geometry : angle 0.73088 / 0.37 ( 9398) SS BOND : bond 0.00721 / 0.32 ( 7) SS BOND : angle 1.71375 / 0.97 ( 14) hydrogen bonds : bond 0.03911 / 2.44 ( 154) hydrogen bonds : angle 6.75577 / 4.63 ( 402) link_BETA1-4 : bond 0.01076 / 0.57 ( 1) link_BETA1-4 : angle 4.80318 / 2.62 ( 3) link_NAG-ASN : bond 0.00113 / 0.05 ( 2) link_NAG-ASN : angle 1.38103 / 0.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 251 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 53 poor density : 198 time to evaluate : 0.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8176 (m) cc_final: 0.7715 (p) REVERT: B 63 LYS cc_start: 0.9311 (tttm) cc_final: 0.8883 (tttp) REVERT: B 89 GLU cc_start: 0.7600 (mp0) cc_final: 0.7237 (mp0) REVERT: C 18 ARG cc_start: 0.4895 (OUTLIER) cc_final: 0.4023 (ttp-110) REVERT: C 54 ARG cc_start: 0.7739 (ptp90) cc_final: 0.7489 (ptp90) REVERT: D 6 GLN cc_start: 0.7782 (tp-100) cc_final: 0.7503 (tm-30) REVERT: D 60 TYR cc_start: 0.8887 (m-10) cc_final: 0.8615 (m-80) REVERT: F 472 ILE cc_start: 0.6377 (mm) cc_final: 0.6142 (mm) REVERT: H 38 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8523 (ttmm) REVERT: I 21 MET cc_start: 0.5838 (mmm) cc_final: 0.5432 (mmm) REVERT: I 97 TYR cc_start: 0.8597 (OUTLIER) cc_final: 0.8170 (p90) REVERT: L 38 LYS cc_start: 0.9194 (tppp) cc_final: 0.8654 (ttpt) outliers start: 53 outliers final: 34 residues processed: 221 average time/residue: 0.0657 time to fit residues: 19.0119 Evaluate side-chains 225 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 188 time to evaluate : 0.183 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 53 LEU Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 30 optimal weight: 0.6980 chunk 49 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 46 optimal weight: 0.9980 chunk 66 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 68 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 8 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... I 27 GLN I 95 GLN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.139133 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.106692 restraints weight = 12571.523| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.110334 restraints weight = 7889.561| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.112809 restraints weight = 5858.597| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114531 restraints weight = 4835.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.115688 restraints weight = 4235.008| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6932 Z= 0.151 Angle : 0.692 13.260 9421 Z= 0.344 Chirality : 0.044 0.194 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.921 50.043 952 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.27 % Rotamer: Outliers : 5.90 % Allowed : 23.46 % Favored : 70.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.37 (0.28), residues: 847 helix: -5.02 (0.62), residues: 8 sheet: -0.52 (0.28), residues: 351 loop : -2.43 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 24 TYR 0.028 0.002 TYR F 380 PHE 0.029 0.002 PHE I 77 TRP 0.010 0.001 TRP H 50 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.15 ( 6922) covalent geometry : angle 0.68235 / 0.34 ( 9398) SS BOND : bond 0.00888 / 0.42 ( 7) SS BOND : angle 2.11296 / 1.30 ( 14) hydrogen bonds : bond 0.03416 / 2.13 ( 154) hydrogen bonds : angle 6.33464 / 4.33 ( 402) link_BETA1-4 : bond 0.01170 / 0.62 ( 1) link_BETA1-4 : angle 4.79259 / 2.62 ( 3) link_NAG-ASN : bond 0.00064 / 0.03 ( 2) link_NAG-ASN : angle 1.29708 / 0.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 242 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 199 time to evaluate : 0.218 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8223 (m) cc_final: 0.7814 (p) REVERT: B 38 LYS cc_start: 0.7782 (ttpp) cc_final: 0.7165 (ttpp) REVERT: B 63 LYS cc_start: 0.9296 (tttm) cc_final: 0.8990 (tttm) REVERT: B 89 GLU cc_start: 0.7608 (mp0) cc_final: 0.7240 (mp0) REVERT: C 18 ARG cc_start: 0.4889 (OUTLIER) cc_final: 0.4425 (ttp80) REVERT: C 54 ARG cc_start: 0.7731 (ptp90) cc_final: 0.7478 (ptp90) REVERT: D 6 GLN cc_start: 0.7756 (tp-100) cc_final: 0.7513 (tm-30) REVERT: D 60 TYR cc_start: 0.8870 (m-10) cc_final: 0.8306 (m-10) REVERT: H 38 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8457 (ttmm) REVERT: H 89 GLU cc_start: 0.8569 (pm20) cc_final: 0.8356 (pm20) REVERT: I 34 ASN cc_start: 0.8498 (p0) cc_final: 0.8026 (p0) REVERT: L 38 LYS cc_start: 0.9170 (tppp) cc_final: 0.8666 (ttpt) outliers start: 43 outliers final: 30 residues processed: 226 average time/residue: 0.0674 time to fit residues: 20.0541 Evaluate side-chains 224 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 192 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 52 optimal weight: 3.9990 chunk 42 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 79 optimal weight: 0.0010 chunk 39 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.1390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 ASN ** H 118 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 95 GLN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.138531 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3383 r_free = 0.3383 target = 0.105675 restraints weight = 12601.532| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.109171 restraints weight = 7965.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.111703 restraints weight = 5985.100| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3491 r_free = 0.3491 target = 0.113406 restraints weight = 4947.324| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.3507 r_free = 0.3507 target = 0.114577 restraints weight = 4343.767| |-----------------------------------------------------------------------------| r_work (final): 0.3507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.3646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6932 Z= 0.183 Angle : 0.717 13.123 9421 Z= 0.355 Chirality : 0.044 0.199 1006 Planarity : 0.004 0.055 1199 Dihedral : 5.953 52.284 952 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 5.90 % Allowed : 24.83 % Favored : 69.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.28), residues: 847 helix: -4.86 (0.75), residues: 8 sheet: -0.46 (0.28), residues: 344 loop : -2.30 (0.26), residues: 495 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG L 24 TYR 0.026 0.002 TYR F 380 PHE 0.023 0.002 PHE I 100 TRP 0.010 0.002 TRP H 50 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00429 / 0.18 ( 6922) covalent geometry : angle 0.70970 / 0.35 ( 9398) SS BOND : bond 0.00672 / 0.30 ( 7) SS BOND : angle 1.56429 / 0.93 ( 14) hydrogen bonds : bond 0.03427 / 2.15 ( 154) hydrogen bonds : angle 6.23210 / 4.28 ( 402) link_BETA1-4 : bond 0.00977 / 0.51 ( 1) link_BETA1-4 : angle 4.61647 / 2.53 ( 3) link_NAG-ASN : bond 0.00062 / 0.03 ( 2) link_NAG-ASN : angle 1.30809 / 0.75 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 236 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 193 time to evaluate : 0.280 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8180 (m) cc_final: 0.7853 (p) REVERT: B 63 LYS cc_start: 0.9345 (tttm) cc_final: 0.8918 (tttm) REVERT: B 89 GLU cc_start: 0.7636 (mp0) cc_final: 0.7287 (mp0) REVERT: C 54 ARG cc_start: 0.7764 (ptp90) cc_final: 0.7475 (ptp90) REVERT: D 6 GLN cc_start: 0.7788 (tp-100) cc_final: 0.7579 (tm-30) REVERT: D 88 SER cc_start: 0.8757 (m) cc_final: 0.8505 (p) REVERT: F 472 ILE cc_start: 0.6211 (mm) cc_final: 0.5964 (mm) REVERT: H 38 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8454 (ttmm) REVERT: I 56 TRP cc_start: 0.7772 (m-10) cc_final: 0.7506 (m-10) REVERT: I 67 ARG cc_start: 0.6249 (OUTLIER) cc_final: 0.5652 (ptt180) REVERT: L 38 LYS cc_start: 0.9187 (tppp) cc_final: 0.8674 (ttpt) outliers start: 43 outliers final: 36 residues processed: 217 average time/residue: 0.0674 time to fit residues: 19.2040 Evaluate side-chains 225 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 187 time to evaluate : 0.153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 LYS Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 78 optimal weight: 7.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 56 optimal weight: 4.9990 chunk 61 optimal weight: 0.9980 chunk 59 optimal weight: 0.8980 chunk 50 optimal weight: 3.9990 chunk 81 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 21 optimal weight: 0.0030 overall best weight: 0.8792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 ASN I 95 GLN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139069 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3394 r_free = 0.3394 target = 0.106346 restraints weight = 12321.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.109901 restraints weight = 7807.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112365 restraints weight = 5851.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113975 restraints weight = 4838.233| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.114931 restraints weight = 4274.816| |-----------------------------------------------------------------------------| r_work (final): 0.3534 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7871 moved from start: 0.3801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6932 Z= 0.155 Angle : 0.703 13.316 9421 Z= 0.348 Chirality : 0.043 0.186 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.855 50.436 952 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 6.45 % Allowed : 24.42 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.17 (0.28), residues: 847 helix: -4.64 (0.95), residues: 8 sheet: -0.43 (0.28), residues: 343 loop : -2.23 (0.26), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG L 24 TYR 0.026 0.002 TYR F 473 PHE 0.024 0.002 PHE I 77 TRP 0.011 0.002 TRP D 36 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.15 ( 6922) covalent geometry : angle 0.69559 / 0.35 ( 9398) SS BOND : bond 0.00639 / 0.28 ( 7) SS BOND : angle 1.50055 / 0.88 ( 14) hydrogen bonds : bond 0.03283 / 2.07 ( 154) hydrogen bonds : angle 6.04232 / 4.14 ( 402) link_BETA1-4 : bond 0.01034 / 0.54 ( 1) link_BETA1-4 : angle 4.56287 / 2.51 ( 3) link_NAG-ASN : bond 0.00057 / 0.03 ( 2) link_NAG-ASN : angle 1.23831 / 0.71 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 198 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8180 (m) cc_final: 0.7916 (p) REVERT: B 38 LYS cc_start: 0.7996 (ttpp) cc_final: 0.7483 (ttmm) REVERT: B 63 LYS cc_start: 0.9321 (tttm) cc_final: 0.9019 (tttm) REVERT: B 89 GLU cc_start: 0.7662 (mp0) cc_final: 0.7313 (mp0) REVERT: C 54 ARG cc_start: 0.7722 (ptp90) cc_final: 0.7484 (ptp90) REVERT: D 23 LYS cc_start: 0.8217 (tttm) cc_final: 0.7815 (ttmm) REVERT: D 60 TYR cc_start: 0.8917 (m-10) cc_final: 0.8671 (m-10) REVERT: D 88 SER cc_start: 0.8716 (m) cc_final: 0.8486 (p) REVERT: F 414 GLN cc_start: 0.7698 (mp10) cc_final: 0.7462 (mp10) REVERT: F 472 ILE cc_start: 0.6249 (mm) cc_final: 0.6039 (mm) REVERT: H 3 GLN cc_start: 0.8325 (tt0) cc_final: 0.7986 (tm-30) REVERT: H 38 LYS cc_start: 0.8979 (OUTLIER) cc_final: 0.8453 (ttmm) REVERT: I 67 ARG cc_start: 0.6116 (OUTLIER) cc_final: 0.5542 (ptt180) REVERT: L 38 LYS cc_start: 0.9193 (tppp) cc_final: 0.8699 (ttpt) outliers start: 47 outliers final: 36 residues processed: 222 average time/residue: 0.0673 time to fit residues: 19.8190 Evaluate side-chains 228 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 190 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 4.9990 chunk 72 optimal weight: 7.9990 chunk 68 optimal weight: 9.9990 chunk 25 optimal weight: 0.4980 chunk 64 optimal weight: 0.7980 chunk 30 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 15 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 22 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 overall best weight: 0.8702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 20 ASN I 95 GLN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3859 r_free = 0.3859 target = 0.140314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.108070 restraints weight = 12405.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.111698 restraints weight = 7752.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.114181 restraints weight = 5756.152| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115900 restraints weight = 4723.307| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116838 restraints weight = 4133.563| |-----------------------------------------------------------------------------| r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6932 Z= 0.153 Angle : 0.697 12.701 9421 Z= 0.344 Chirality : 0.043 0.181 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.827 48.999 952 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 10.84 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.56 % Favored : 92.33 % Rotamer: Outliers : 6.17 % Allowed : 24.42 % Favored : 69.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.11 (0.28), residues: 847 helix: -4.48 (1.10), residues: 8 sheet: -0.32 (0.28), residues: 349 loop : -2.27 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.023 0.002 TYR C 91 PHE 0.022 0.002 PHE I 77 TRP 0.023 0.002 TRP I 56 HIS 0.003 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00360 / 0.15 ( 6922) covalent geometry : angle 0.69109 / 0.34 ( 9398) SS BOND : bond 0.00531 / 0.22 ( 7) SS BOND : angle 1.18039 / 0.67 ( 14) hydrogen bonds : bond 0.03224 / 2.05 ( 154) hydrogen bonds : angle 6.01273 / 4.15 ( 402) link_BETA1-4 : bond 0.01062 / 0.56 ( 1) link_BETA1-4 : angle 4.42657 / 2.44 ( 3) link_NAG-ASN : bond 0.00076 / 0.04 ( 2) link_NAG-ASN : angle 1.21163 / 0.70 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 196 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8250 (m) cc_final: 0.8033 (p) REVERT: B 38 LYS cc_start: 0.8099 (ttpp) cc_final: 0.7525 (ttmm) REVERT: B 89 GLU cc_start: 0.7674 (mp0) cc_final: 0.7309 (mp0) REVERT: C 54 ARG cc_start: 0.7694 (ptp90) cc_final: 0.7431 (ptp90) REVERT: D 23 LYS cc_start: 0.8275 (tttm) cc_final: 0.7862 (ttmm) REVERT: D 60 TYR cc_start: 0.8815 (m-10) cc_final: 0.8316 (m-80) REVERT: F 414 GLN cc_start: 0.7699 (mp10) cc_final: 0.7481 (mp10) REVERT: F 472 ILE cc_start: 0.6299 (mm) cc_final: 0.6052 (mm) REVERT: H 3 GLN cc_start: 0.8328 (tt0) cc_final: 0.8010 (tm-30) REVERT: H 38 LYS cc_start: 0.8981 (OUTLIER) cc_final: 0.8476 (ttmm) REVERT: I 67 ARG cc_start: 0.6162 (OUTLIER) cc_final: 0.5597 (ptt180) REVERT: L 38 LYS cc_start: 0.9208 (tppp) cc_final: 0.8713 (ttpt) outliers start: 45 outliers final: 37 residues processed: 219 average time/residue: 0.0707 time to fit residues: 20.4122 Evaluate side-chains 227 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 188 time to evaluate : 0.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 1.9990 chunk 55 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 72 optimal weight: 0.9990 chunk 69 optimal weight: 9.9990 chunk 78 optimal weight: 0.0770 overall best weight: 0.7140 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 6 GLN C 20 ASN I 95 GLN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.140257 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3414 r_free = 0.3414 target = 0.107549 restraints weight = 12485.455| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3465 r_free = 0.3465 target = 0.111186 restraints weight = 7891.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.113645 restraints weight = 5907.244| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115369 restraints weight = 4883.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116415 restraints weight = 4285.152| |-----------------------------------------------------------------------------| r_work (final): 0.3556 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.4089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6932 Z= 0.143 Angle : 0.720 12.481 9421 Z= 0.355 Chirality : 0.044 0.323 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.772 52.183 952 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.73 % Favored : 93.15 % Rotamer: Outliers : 5.90 % Allowed : 26.20 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.28), residues: 847 helix: -4.76 (0.77), residues: 14 sheet: -0.14 (0.29), residues: 324 loop : -2.15 (0.26), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.022 0.002 TYR F 473 PHE 0.031 0.002 PHE I 77 TRP 0.027 0.002 TRP I 56 HIS 0.002 0.001 HIS B 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00339 / 0.14 ( 6922) covalent geometry : angle 0.71445 / 0.35 ( 9398) SS BOND : bond 0.00501 / 0.20 ( 7) SS BOND : angle 1.10291 / 0.62 ( 14) hydrogen bonds : bond 0.03270 / 2.05 ( 154) hydrogen bonds : angle 5.93397 / 4.08 ( 402) link_BETA1-4 : bond 0.01020 / 0.54 ( 1) link_BETA1-4 : angle 4.35729 / 2.41 ( 3) link_NAG-ASN : bond 0.00065 / 0.03 ( 2) link_NAG-ASN : angle 1.20431 / 0.69 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 188 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8235 (m) cc_final: 0.8005 (p) REVERT: B 38 LYS cc_start: 0.8055 (ttpp) cc_final: 0.7534 (ttmm) REVERT: B 89 GLU cc_start: 0.7677 (mp0) cc_final: 0.7348 (mp0) REVERT: C 20 ASN cc_start: 0.6808 (OUTLIER) cc_final: 0.6607 (p0) REVERT: D 23 LYS cc_start: 0.8262 (tttm) cc_final: 0.7869 (ttmm) REVERT: D 60 TYR cc_start: 0.8849 (m-10) cc_final: 0.8309 (m-80) REVERT: F 472 ILE cc_start: 0.6216 (mm) cc_final: 0.6001 (mm) REVERT: H 38 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8480 (ttmm) REVERT: I 67 ARG cc_start: 0.6064 (OUTLIER) cc_final: 0.5520 (ptt180) REVERT: L 38 LYS cc_start: 0.9208 (tppp) cc_final: 0.8701 (ttpt) REVERT: L 78 GLU cc_start: 0.8370 (tt0) cc_final: 0.7961 (tt0) outliers start: 43 outliers final: 35 residues processed: 210 average time/residue: 0.0701 time to fit residues: 19.2640 Evaluate side-chains 218 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 180 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 14 SER Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 20 ASN Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 40 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 36 optimal weight: 0.4980 chunk 70 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 29 optimal weight: 0.0980 chunk 33 optimal weight: 0.9980 chunk 78 optimal weight: 8.9990 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... H 3 GLN I 95 GLN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.140126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.107219 restraints weight = 12334.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111027 restraints weight = 7559.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3497 r_free = 0.3497 target = 0.113658 restraints weight = 5556.490| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.3521 r_free = 0.3521 target = 0.115436 restraints weight = 4534.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.116573 restraints weight = 3958.476| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6932 Z= 0.136 Angle : 0.721 11.833 9421 Z= 0.358 Chirality : 0.044 0.275 1006 Planarity : 0.004 0.053 1199 Dihedral : 5.817 54.137 952 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 5.08 % Allowed : 26.47 % Favored : 68.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.97 (0.28), residues: 847 helix: -4.70 (0.83), residues: 14 sheet: -0.18 (0.29), residues: 331 loop : -2.10 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG L 24 TYR 0.025 0.002 TYR F 380 PHE 0.030 0.001 PHE I 77 TRP 0.052 0.002 TRP I 56 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00322 / 0.14 ( 6922) covalent geometry : angle 0.71625 / 0.36 ( 9398) SS BOND : bond 0.00460 / 0.18 ( 7) SS BOND : angle 1.00947 / 0.56 ( 14) hydrogen bonds : bond 0.03173 / 1.98 ( 154) hydrogen bonds : angle 5.84361 / 4.00 ( 402) link_BETA1-4 : bond 0.00932 / 0.49 ( 1) link_BETA1-4 : angle 4.29860 / 2.37 ( 3) link_NAG-ASN : bond 0.00089 / 0.05 ( 2) link_NAG-ASN : angle 1.17222 / 0.68 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 184 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8335 (m) cc_final: 0.8128 (p) REVERT: B 38 LYS cc_start: 0.7959 (ttpp) cc_final: 0.7405 (ttmm) REVERT: B 89 GLU cc_start: 0.7693 (mp0) cc_final: 0.7353 (mp0) REVERT: C 63 THR cc_start: 0.7619 (p) cc_final: 0.7416 (p) REVERT: D 10 GLU cc_start: 0.7141 (tm-30) cc_final: 0.6396 (tm-30) REVERT: D 23 LYS cc_start: 0.8254 (tttm) cc_final: 0.7852 (ttmm) REVERT: D 60 TYR cc_start: 0.8844 (m-10) cc_final: 0.8350 (m-80) REVERT: H 38 LYS cc_start: 0.8969 (OUTLIER) cc_final: 0.8487 (ttmm) REVERT: L 38 LYS cc_start: 0.9218 (tppp) cc_final: 0.8694 (ttpt) outliers start: 37 outliers final: 34 residues processed: 204 average time/residue: 0.0839 time to fit residues: 22.2854 Evaluate side-chains 216 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 181 time to evaluate : 0.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 414 GLN Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 39 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 64 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 PHE Chi-restraints excluded: chain I residue 69 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 64 optimal weight: 2.9990 chunk 75 optimal weight: 0.0970 chunk 3 optimal weight: 0.5980 chunk 79 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 17 optimal weight: 4.9990 chunk 53 optimal weight: 0.5980 chunk 6 optimal weight: 0.1980 chunk 21 optimal weight: 0.5980 chunk 60 optimal weight: 1.9990 chunk 29 optimal weight: 0.4980 overall best weight: 0.3978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 77 ASN H 3 GLN ** I 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3915 r_free = 0.3915 target = 0.143831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.111995 restraints weight = 12433.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3536 r_free = 0.3536 target = 0.115665 restraints weight = 7862.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3570 r_free = 0.3570 target = 0.118114 restraints weight = 5876.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.119785 restraints weight = 4870.515| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.120863 restraints weight = 4290.041| |-----------------------------------------------------------------------------| r_work (final): 0.3635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7765 moved from start: 0.4429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6932 Z= 0.122 Angle : 0.712 11.309 9421 Z= 0.354 Chirality : 0.044 0.237 1006 Planarity : 0.004 0.053 1199 Dihedral : 5.644 54.190 952 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 11.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 4.94 % Allowed : 26.34 % Favored : 68.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.90 (0.28), residues: 847 helix: -4.55 (0.98), residues: 14 sheet: -0.09 (0.29), residues: 333 loop : -2.10 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG L 24 TYR 0.023 0.002 TYR F 380 PHE 0.018 0.001 PHE I 100 TRP 0.039 0.002 TRP I 56 HIS 0.003 0.001 HIS L 33 Details of bonding type rmsd/Z covalent geometry : bond 0.00286 / 0.12 ( 6922) covalent geometry : angle 0.70710 / 0.35 ( 9398) SS BOND : bond 0.00477 / 0.18 ( 7) SS BOND : angle 0.96266 / 0.54 ( 14) hydrogen bonds : bond 0.03109 / 1.97 ( 154) hydrogen bonds : angle 5.65671 / 3.87 ( 402) link_BETA1-4 : bond 0.00820 / 0.43 ( 1) link_BETA1-4 : angle 4.21931 / 2.34 ( 3) link_NAG-ASN : bond 0.00069 / 0.03 ( 2) link_NAG-ASN : angle 1.10776 / 0.64 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1262.61 seconds wall clock time: 22 minutes 29.97 seconds (1349.97 seconds total)