Starting phenix.real_space_refine on Tue Mar 11 23:02:25 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wp6_32676/03_2025/7wp6_32676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp6_32676/03_2025/7wp6_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7wp6_32676/03_2025/7wp6_32676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp6_32676/03_2025/7wp6_32676.map" model { file = "/net/cci-nas-00/data/ceres_data/7wp6_32676/03_2025/7wp6_32676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp6_32676/03_2025/7wp6_32676.cif" } resolution = 3.81 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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 dihedrals: 6 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 dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.48, per 1000 atoms: 0.81 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: 1.61 Conformation dependent library (CDL) restraints added in 970.0 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: 0.88 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: 1.83 Time building geometry restraints manager: 1.93 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: 3544 16.61 - 33.21: 450 33.21 - 49.82: 75 49.82 - 66.43: 12 66.43 - 83.03: 9 Dihedral angle restraints: 4090 sinusoidal: 1608 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 4087 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: 4.040 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: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.830 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 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 : 0.008 0.061 6922 Z= 0.493 Angle : 1.066 15.738 9398 Z= 0.594 Chirality : 0.062 0.397 1006 Planarity : 0.013 0.284 1199 Dihedral : 14.824 83.035 2501 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -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 TRP 0.027 0.003 TRP I 56 HIS 0.006 0.003 HIS H 35 PHE 0.029 0.003 PHE I 100 TYR 0.032 0.003 TYR I 55 ARG 0.006 0.001 ARG F 355 *********************** 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 : 0.722 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: 0.8229 (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: 0.2161 time to fit residues: 67.4461 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 : 0.756 ------------------------------------------------------------------------------- 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 69 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 chunk 64 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 47 optimal weight: 0.4980 chunk 74 optimal weight: 3.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 GLN C 79 GLN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 62 GLN F 487 ASN F 493 GLN ** I 96 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.140739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3415 r_free = 0.3415 target = 0.107862 restraints weight = 12339.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111494 restraints weight = 7828.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114021 restraints weight = 5868.529| |-----------------------------------------------------------------------------| r_work (final): 0.3500 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.2397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6922 Z= 0.219 Angle : 0.683 12.368 9398 Z= 0.350 Chirality : 0.045 0.215 1006 Planarity : 0.005 0.059 1199 Dihedral : 6.271 41.933 1015 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.26 % Favored : 93.62 % Rotamer: Outliers : 3.57 % Allowed : 21.26 % Favored : 75.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.99 (0.27), residues: 847 helix: -5.23 (0.43), residues: 8 sheet: -1.01 (0.28), residues: 356 loop : -2.82 (0.24), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP I 56 HIS 0.003 0.001 HIS L 33 PHE 0.026 0.002 PHE I 100 TYR 0.020 0.002 TYR I 42 ARG 0.003 0.001 ARG C 61 *********************** 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 239 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 213 time to evaluate : 0.767 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7762 (m-80) cc_final: 0.7377 (m-80) REVERT: B 89 GLU cc_start: 0.7474 (mp0) cc_final: 0.7207 (mp0) REVERT: C 18 ARG cc_start: 0.4614 (OUTLIER) cc_final: 0.3802 (ttp-110) REVERT: C 54 ARG cc_start: 0.7753 (ptp90) cc_final: 0.7537 (ptp90) REVERT: D 60 TYR cc_start: 0.8845 (m-10) cc_final: 0.8446 (m-80) REVERT: D 80 TYR cc_start: 0.7877 (m-80) cc_final: 0.7590 (m-10) REVERT: F 414 GLN cc_start: 0.7398 (tt0) cc_final: 0.7051 (mp10) REVERT: H 38 LYS cc_start: 0.8915 (ttmm) cc_final: 0.8333 (ttmm) REVERT: I 41 TRP cc_start: 0.8558 (m100) cc_final: 0.8265 (m100) REVERT: I 56 TRP cc_start: 0.7125 (m100) cc_final: 0.6102 (m100) REVERT: L 38 LYS cc_start: 0.9189 (tppp) cc_final: 0.8664 (ttpt) outliers start: 26 outliers final: 20 residues processed: 222 average time/residue: 0.2108 time to fit residues: 59.8830 Evaluate side-chains 206 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 185 time to evaluate : 0.764 ------------------------------------------------------------------------------- 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 D residue 71 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 69 THR 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 14 optimal weight: 1.9990 chunk 75 optimal weight: 1.9990 chunk 67 optimal weight: 0.0970 chunk 33 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 4 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 29 optimal weight: 4.9990 chunk 64 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 23 optimal weight: 3.9990 overall best weight: 1.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 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 = 0.3806 r_free = 0.3806 target = 0.136170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.103424 restraints weight = 12546.067| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.106851 restraints weight = 8112.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109190 restraints weight = 6175.767| |-----------------------------------------------------------------------------| r_work (final): 0.3458 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.2790 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 6922 Z= 0.351 Angle : 0.734 13.940 9398 Z= 0.372 Chirality : 0.045 0.233 1006 Planarity : 0.005 0.058 1199 Dihedral : 6.395 52.356 1015 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 13.19 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.91 % Favored : 91.97 % Rotamer: Outliers : 6.45 % Allowed : 20.71 % Favored : 72.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.73 (0.27), residues: 847 helix: -5.20 (0.46), residues: 8 sheet: -0.79 (0.28), residues: 356 loop : -2.68 (0.25), residues: 483 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 56 HIS 0.006 0.001 HIS L 33 PHE 0.026 0.002 PHE I 100 TYR 0.024 0.002 TYR I 97 ARG 0.004 0.001 ARG H 40 *********************** 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 246 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 47 poor density : 199 time to evaluate : 0.771 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 63 LYS cc_start: 0.9262 (tttm) cc_final: 0.8945 (tttm) REVERT: B 89 GLU cc_start: 0.7556 (mp0) cc_final: 0.7202 (mp0) REVERT: C 14 SER cc_start: 0.7687 (t) cc_final: 0.7067 (t) REVERT: C 18 ARG cc_start: 0.4845 (OUTLIER) cc_final: 0.4409 (ttp-110) REVERT: D 60 TYR cc_start: 0.8887 (m-10) cc_final: 0.8626 (m-80) REVERT: D 80 TYR cc_start: 0.7885 (m-80) cc_final: 0.7587 (m-10) REVERT: F 414 GLN cc_start: 0.7470 (tt0) cc_final: 0.7123 (mp10) REVERT: F 472 ILE cc_start: 0.6415 (mm) cc_final: 0.6181 (mm) REVERT: H 38 LYS cc_start: 0.9001 (ttmm) cc_final: 0.8577 (ttmm) REVERT: I 41 TRP cc_start: 0.8561 (m100) cc_final: 0.8265 (m100) REVERT: I 51 LYS cc_start: 0.9130 (tptt) cc_final: 0.8907 (tptt) REVERT: L 21 MET cc_start: 0.7263 (ptp) cc_final: 0.6846 (mtm) REVERT: L 38 LYS cc_start: 0.9228 (tppp) cc_final: 0.8686 (ttpt) outliers start: 47 outliers final: 34 residues processed: 221 average time/residue: 0.2231 time to fit residues: 63.4462 Evaluate side-chains 222 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.785 ------------------------------------------------------------------------------- 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 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 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 46 LEU 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 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 425 LEU Chi-restraints excluded: chain F residue 478 THR 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 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 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 95 GLN Chi-restraints excluded: chain I residue 108 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 22 optimal weight: 5.9990 chunk 69 optimal weight: 0.7980 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.0980 chunk 30 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 41 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 96 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 = 0.3807 r_free = 0.3807 target = 0.136410 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.103894 restraints weight = 12659.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.107412 restraints weight = 8089.127| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.109773 restraints weight = 6119.592| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.3119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 6922 Z= 0.303 Angle : 0.707 13.626 9398 Z= 0.355 Chirality : 0.044 0.228 1006 Planarity : 0.005 0.054 1199 Dihedral : 6.378 57.078 1015 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.67 % Favored : 92.21 % Rotamer: Outliers : 6.04 % Allowed : 22.50 % Favored : 71.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.58 (0.28), residues: 847 helix: -5.13 (0.51), residues: 8 sheet: -0.61 (0.28), residues: 346 loop : -2.61 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP I 56 HIS 0.004 0.001 HIS L 33 PHE 0.026 0.002 PHE I 100 TYR 0.022 0.002 TYR I 97 ARG 0.004 0.001 ARG L 24 *********************** 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 238 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 194 time to evaluate : 0.769 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8237 (m) cc_final: 0.7816 (p) REVERT: B 63 LYS cc_start: 0.9308 (tttm) cc_final: 0.8866 (tttp) REVERT: B 89 GLU cc_start: 0.7616 (mp0) cc_final: 0.7222 (mp0) REVERT: D 10 GLU cc_start: 0.7223 (tm-30) cc_final: 0.6197 (tm-30) REVERT: D 60 TYR cc_start: 0.8864 (m-10) cc_final: 0.8356 (m-10) REVERT: D 80 TYR cc_start: 0.7880 (m-80) cc_final: 0.7623 (m-10) REVERT: F 414 GLN cc_start: 0.7425 (tt0) cc_final: 0.7143 (mp10) REVERT: F 472 ILE cc_start: 0.6352 (mm) cc_final: 0.6113 (mm) REVERT: H 38 LYS cc_start: 0.9021 (OUTLIER) cc_final: 0.8459 (ttmm) REVERT: I 21 MET cc_start: 0.5878 (mmm) cc_final: 0.5590 (mmm) REVERT: I 36 LYS cc_start: 0.6979 (mtpt) cc_final: 0.6732 (mtpt) REVERT: I 41 TRP cc_start: 0.8497 (m100) cc_final: 0.8168 (m100) REVERT: I 97 TYR cc_start: 0.8663 (OUTLIER) cc_final: 0.7851 (p90) REVERT: L 38 LYS cc_start: 0.9200 (tppp) cc_final: 0.8654 (ttpt) outliers start: 44 outliers final: 32 residues processed: 216 average time/residue: 0.1953 time to fit residues: 54.8785 Evaluate side-chains 219 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 185 time to evaluate : 0.700 ------------------------------------------------------------------------------- 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 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 46 LEU 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 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 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 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 95 GLN Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 32 MET Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 17 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 67 optimal weight: 3.9990 chunk 57 optimal weight: 10.0000 chunk 32 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 50 optimal weight: 4.9990 chunk 48 optimal weight: 0.0570 chunk 21 optimal weight: 0.0980 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.4500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 GLN I 96 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 = 0.3855 r_free = 0.3855 target = 0.140269 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3416 r_free = 0.3416 target = 0.107857 restraints weight = 12214.562| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.111404 restraints weight = 7712.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.113914 restraints weight = 5777.807| |-----------------------------------------------------------------------------| r_work (final): 0.3520 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7751 moved from start: 0.3468 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6922 Z= 0.176 Angle : 0.655 13.106 9398 Z= 0.327 Chirality : 0.043 0.182 1006 Planarity : 0.004 0.053 1199 Dihedral : 5.923 53.843 1015 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 10.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer: Outliers : 5.08 % Allowed : 24.42 % Favored : 70.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.37 (0.28), residues: 847 helix: -4.86 (0.72), residues: 8 sheet: -0.47 (0.28), residues: 351 loop : -2.48 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP I 56 HIS 0.002 0.001 HIS B 35 PHE 0.023 0.001 PHE I 100 TYR 0.025 0.001 TYR F 380 ARG 0.002 0.000 ARG B 84 *********************** 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 236 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 199 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8247 (m) cc_final: 0.7838 (p) REVERT: B 63 LYS cc_start: 0.9289 (tttm) cc_final: 0.9010 (tttm) REVERT: B 81 MET cc_start: 0.7067 (ttm) cc_final: 0.6676 (ttm) REVERT: B 89 GLU cc_start: 0.7590 (mp0) cc_final: 0.7236 (mp0) REVERT: D 23 LYS cc_start: 0.8175 (tttm) cc_final: 0.7803 (ttmm) REVERT: D 80 TYR cc_start: 0.7883 (m-80) cc_final: 0.7662 (m-10) REVERT: F 414 GLN cc_start: 0.7270 (tt0) cc_final: 0.6984 (mp10) REVERT: F 472 ILE cc_start: 0.6221 (mm) cc_final: 0.5978 (mm) REVERT: H 3 GLN cc_start: 0.8391 (tt0) cc_final: 0.7899 (tm-30) REVERT: H 38 LYS cc_start: 0.9001 (OUTLIER) cc_final: 0.8484 (ttmm) REVERT: H 89 GLU cc_start: 0.8603 (pm20) cc_final: 0.8371 (pm20) REVERT: I 56 TRP cc_start: 0.7791 (m-10) cc_final: 0.7544 (m-10) REVERT: L 38 LYS cc_start: 0.9178 (tppp) cc_final: 0.8639 (ttpt) outliers start: 37 outliers final: 29 residues processed: 218 average time/residue: 0.2014 time to fit residues: 56.8339 Evaluate side-chains 217 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 187 time to evaluate : 0.720 ------------------------------------------------------------------------------- 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 37 VAL Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 27 GLN 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 114 THR Chi-restraints excluded: chain F residue 368 LEU 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 42 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 95 GLN Chi-restraints excluded: chain I residue 108 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 Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.0370 chunk 49 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 18 optimal weight: 5.9990 chunk 32 optimal weight: 0.0040 overall best weight: 1.0076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN B 41 HIS C 20 ASN I 27 GLN ** I 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.138089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.105288 restraints weight = 12360.732| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3427 r_free = 0.3427 target = 0.108742 restraints weight = 7943.066| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.111173 restraints weight = 6017.820| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7818 moved from start: 0.3597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6922 Z= 0.248 Angle : 0.684 13.458 9398 Z= 0.340 Chirality : 0.043 0.192 1006 Planarity : 0.004 0.056 1199 Dihedral : 6.008 57.982 1015 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 5.76 % Allowed : 25.65 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.28), residues: 847 helix: -4.63 (0.92), residues: 8 sheet: -0.29 (0.28), residues: 349 loop : -2.36 (0.26), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP I 56 HIS 0.003 0.001 HIS B 35 PHE 0.023 0.002 PHE I 100 TYR 0.021 0.002 TYR I 42 ARG 0.004 0.001 ARG C 54 *********************** 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 235 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 193 time to evaluate : 0.744 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8201 (m) cc_final: 0.7873 (p) REVERT: B 63 LYS cc_start: 0.9311 (tttm) cc_final: 0.8952 (tttm) REVERT: B 89 GLU cc_start: 0.7580 (mp0) cc_final: 0.7256 (mp0) REVERT: D 23 LYS cc_start: 0.8234 (tttm) cc_final: 0.7853 (ttmm) REVERT: F 414 GLN cc_start: 0.7341 (tt0) cc_final: 0.7056 (mp10) REVERT: F 472 ILE cc_start: 0.6298 (mm) cc_final: 0.6068 (mm) REVERT: H 3 GLN cc_start: 0.8383 (tt0) cc_final: 0.7918 (tm-30) REVERT: H 38 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8477 (ttmm) REVERT: I 56 TRP cc_start: 0.7812 (m-10) cc_final: 0.7600 (m-10) REVERT: L 38 LYS cc_start: 0.9199 (tppp) cc_final: 0.8684 (ttpt) outliers start: 42 outliers final: 36 residues processed: 215 average time/residue: 0.1936 time to fit residues: 54.0757 Evaluate side-chains 222 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 185 time to evaluate : 0.761 ------------------------------------------------------------------------------- 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 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 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 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 95 GLN Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 33 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 0.0570 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 7.9990 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 4.9990 chunk 64 optimal weight: 0.9990 overall best weight: 1.1904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 HIS I 27 GLN I 34 ASN L 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3820 r_free = 0.3820 target = 0.137479 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3371 r_free = 0.3371 target = 0.104868 restraints weight = 12436.780| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108236 restraints weight = 8113.798| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3452 r_free = 0.3452 target = 0.110561 restraints weight = 6183.479| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.3792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 6922 Z= 0.278 Angle : 0.708 12.995 9398 Z= 0.351 Chirality : 0.044 0.198 1006 Planarity : 0.004 0.057 1199 Dihedral : 6.071 50.142 1015 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.79 % Favored : 92.09 % Rotamer: Outliers : 7.00 % Allowed : 24.01 % Favored : 69.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.12 (0.28), residues: 847 helix: -4.52 (1.04), residues: 8 sheet: -0.39 (0.29), residues: 337 loop : -2.18 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP H 50 HIS 0.003 0.001 HIS B 35 PHE 0.022 0.002 PHE I 100 TYR 0.020 0.002 TYR I 42 ARG 0.003 0.001 ARG L 76 *********************** 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 239 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 188 time to evaluate : 0.637 Fit side-chains REVERT: B 17 SER cc_start: 0.8299 (m) cc_final: 0.8073 (p) REVERT: B 63 LYS cc_start: 0.9368 (tttm) cc_final: 0.9005 (tttm) REVERT: B 89 GLU cc_start: 0.7635 (mp0) cc_final: 0.7274 (mp0) REVERT: C 47 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8165 (mp) REVERT: D 23 LYS cc_start: 0.8263 (tttm) cc_final: 0.7888 (ttmm) REVERT: F 414 GLN cc_start: 0.7352 (tt0) cc_final: 0.7050 (mp10) REVERT: F 472 ILE cc_start: 0.6350 (mm) cc_final: 0.6118 (mm) REVERT: H 3 GLN cc_start: 0.8387 (tt0) cc_final: 0.7930 (tm-30) REVERT: H 38 LYS cc_start: 0.9016 (OUTLIER) cc_final: 0.8484 (ttmm) REVERT: I 21 MET cc_start: 0.5767 (mmm) cc_final: 0.5297 (mmm) REVERT: I 56 TRP cc_start: 0.7881 (m-10) cc_final: 0.7618 (m-10) REVERT: I 67 ARG cc_start: 0.6278 (OUTLIER) cc_final: 0.5796 (ptt180) REVERT: I 97 TYR cc_start: 0.8670 (OUTLIER) cc_final: 0.7937 (p90) REVERT: L 38 LYS cc_start: 0.9200 (tppp) cc_final: 0.8665 (ttpt) outliers start: 51 outliers final: 40 residues processed: 214 average time/residue: 0.2105 time to fit residues: 58.5175 Evaluate side-chains 225 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 181 time to evaluate : 0.707 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 33 THR 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 47 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 78 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 474 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 69 THR 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 29 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 I residue 95 GLN Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 21 MET Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 38 optimal weight: 0.9980 chunk 12 optimal weight: 6.9990 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 65 optimal weight: 0.0970 chunk 59 optimal weight: 0.6980 chunk 35 optimal weight: 5.9990 chunk 42 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 5.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 27 GLN L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3853 r_free = 0.3853 target = 0.140046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.107284 restraints weight = 12438.540| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.110924 restraints weight = 7871.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.113469 restraints weight = 5902.546| |-----------------------------------------------------------------------------| r_work (final): 0.3488 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7760 moved from start: 0.3993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6922 Z= 0.194 Angle : 0.682 12.049 9398 Z= 0.337 Chirality : 0.043 0.171 1006 Planarity : 0.004 0.055 1199 Dihedral : 5.791 49.891 1015 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 5.76 % Allowed : 24.83 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.96 (0.28), residues: 847 helix: -4.16 (1.37), residues: 8 sheet: -0.16 (0.29), residues: 327 loop : -2.15 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 50 HIS 0.002 0.001 HIS H 35 PHE 0.021 0.001 PHE I 100 TYR 0.021 0.002 TYR C 91 ARG 0.004 0.000 ARG C 54 *********************** 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 236 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 194 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8372 (m) cc_final: 0.8161 (p) REVERT: B 34 MET cc_start: 0.7691 (mmm) cc_final: 0.7289 (mtt) REVERT: B 89 GLU cc_start: 0.7640 (mp0) cc_final: 0.7298 (mp0) REVERT: C 47 LEU cc_start: 0.8336 (OUTLIER) cc_final: 0.8016 (mp) REVERT: D 23 LYS cc_start: 0.8263 (tttm) cc_final: 0.7797 (ttmm) REVERT: F 414 GLN cc_start: 0.7318 (tt0) cc_final: 0.6978 (mp10) REVERT: F 472 ILE cc_start: 0.6224 (mm) cc_final: 0.6004 (mm) REVERT: H 38 LYS cc_start: 0.8998 (OUTLIER) cc_final: 0.8475 (ttmm) REVERT: H 69 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8518 (p) REVERT: I 21 MET cc_start: 0.5787 (mmm) cc_final: 0.5422 (mmm) REVERT: I 56 TRP cc_start: 0.7790 (m-10) cc_final: 0.7579 (m-10) REVERT: I 97 TYR cc_start: 0.8759 (OUTLIER) cc_final: 0.8005 (p90) REVERT: L 38 LYS cc_start: 0.9193 (tppp) cc_final: 0.8606 (ttpt) outliers start: 42 outliers final: 31 residues processed: 212 average time/residue: 0.1984 time to fit residues: 54.3240 Evaluate side-chains 220 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 185 time to evaluate : 0.782 ------------------------------------------------------------------------------- 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 17 ASP Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 47 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 76 SER 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 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 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 36 LYS 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 I residue 95 GLN Chi-restraints excluded: chain I residue 97 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 7 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 13 optimal weight: 0.9990 chunk 65 optimal weight: 0.9990 chunk 35 optimal weight: 5.9990 chunk 37 optimal weight: 0.5980 chunk 63 optimal weight: 6.9990 chunk 76 optimal weight: 0.0370 chunk 41 optimal weight: 0.3980 chunk 74 optimal weight: 5.9990 chunk 46 optimal weight: 0.0770 overall best weight: 0.4218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN H 3 GLN I 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3880 r_free = 0.3880 target = 0.142263 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.109434 restraints weight = 12429.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3490 r_free = 0.3490 target = 0.113152 restraints weight = 7841.130| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.115713 restraints weight = 5852.112| |-----------------------------------------------------------------------------| r_work (final): 0.3519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 moved from start: 0.4249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6922 Z= 0.176 Angle : 0.679 11.414 9398 Z= 0.336 Chirality : 0.044 0.331 1006 Planarity : 0.004 0.055 1199 Dihedral : 5.473 49.212 1015 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.49 % Favored : 93.51 % Rotamer: Outliers : 5.21 % Allowed : 26.34 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.89 (0.28), residues: 847 helix: -4.51 (0.99), residues: 14 sheet: -0.12 (0.29), residues: 326 loop : -2.03 (0.26), residues: 507 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 36 HIS 0.002 0.001 HIS C 55 PHE 0.019 0.001 PHE I 100 TYR 0.020 0.001 TYR I 42 ARG 0.006 0.001 ARG L 76 *********************** 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 226 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 188 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 MET cc_start: 0.7629 (mmm) cc_final: 0.7263 (mtt) REVERT: B 89 GLU cc_start: 0.7622 (mp0) cc_final: 0.7293 (mp0) REVERT: D 10 GLU cc_start: 0.7115 (tm-30) cc_final: 0.6345 (tm-30) REVERT: D 23 LYS cc_start: 0.8154 (tttm) cc_final: 0.7785 (ttmm) REVERT: D 80 TYR cc_start: 0.7775 (m-80) cc_final: 0.7544 (m-10) REVERT: F 398 ASP cc_start: 0.8514 (p0) cc_final: 0.8154 (p0) REVERT: F 414 GLN cc_start: 0.7189 (tt0) cc_final: 0.6978 (mp10) REVERT: H 38 LYS cc_start: 0.8975 (OUTLIER) cc_final: 0.8541 (ttmm) REVERT: H 69 THR cc_start: 0.8936 (OUTLIER) cc_final: 0.8485 (p) REVERT: I 21 MET cc_start: 0.5779 (mmm) cc_final: 0.5487 (mmm) REVERT: I 97 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.7843 (p90) REVERT: L 38 LYS cc_start: 0.9223 (tppp) cc_final: 0.8682 (ttpt) outliers start: 38 outliers final: 32 residues processed: 206 average time/residue: 0.2114 time to fit residues: 56.2197 Evaluate side-chains 217 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 182 time to evaluate : 0.756 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR 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 17 ASP 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 D residue 71 THR Chi-restraints excluded: chain D residue 76 SER 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 474 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 69 THR 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 29 LEU Chi-restraints excluded: chain I residue 36 LYS 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 I residue 97 TYR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 chunk 17 optimal weight: 4.9990 chunk 63 optimal weight: 9.9990 chunk 21 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 101 HIS I 27 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.141018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3419 r_free = 0.3419 target = 0.108106 restraints weight = 12652.753| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.111659 restraints weight = 8161.416| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.114055 restraints weight = 6181.157| |-----------------------------------------------------------------------------| r_work (final): 0.3499 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7756 moved from start: 0.4297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6922 Z= 0.213 Angle : 0.698 11.201 9398 Z= 0.347 Chirality : 0.044 0.230 1006 Planarity : 0.004 0.056 1199 Dihedral : 5.550 47.723 1014 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.20 % Favored : 92.68 % Rotamer: Outliers : 4.94 % Allowed : 26.47 % Favored : 68.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.29), residues: 847 helix: -4.50 (1.00), residues: 14 sheet: -0.06 (0.29), residues: 337 loop : -2.06 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.002 0.001 HIS H 101 PHE 0.025 0.001 PHE D 64 TYR 0.020 0.002 TYR I 42 ARG 0.003 0.001 ARG C 54 ********************** 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 220 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 184 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 MET cc_start: 0.7692 (mmm) cc_final: 0.7256 (mtt) REVERT: B 89 GLU cc_start: 0.7674 (mp0) cc_final: 0.7324 (mp0) REVERT: D 10 GLU cc_start: 0.7168 (tm-30) cc_final: 0.6893 (tm-30) REVERT: D 23 LYS cc_start: 0.8195 (tttm) cc_final: 0.7844 (ttmm) REVERT: D 80 TYR cc_start: 0.7788 (m-80) cc_final: 0.7553 (m-10) REVERT: F 398 ASP cc_start: 0.8470 (p0) cc_final: 0.8109 (p0) REVERT: F 414 GLN cc_start: 0.7228 (tt0) cc_final: 0.7013 (mp10) REVERT: H 38 LYS cc_start: 0.8936 (OUTLIER) cc_final: 0.8516 (ttmm) REVERT: I 21 MET cc_start: 0.5769 (mmm) cc_final: 0.5473 (mmm) REVERT: I 97 TYR cc_start: 0.8647 (OUTLIER) cc_final: 0.7988 (p90) REVERT: L 38 LYS cc_start: 0.9224 (tppp) cc_final: 0.8689 (ttpt) outliers start: 36 outliers final: 31 residues processed: 200 average time/residue: 0.2046 time to fit residues: 52.9975 Evaluate side-chains 217 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 184 time to evaluate : 0.760 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 33 THR 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 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 D residue 71 THR Chi-restraints excluded: chain D residue 76 SER 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 474 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 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 27 GLN Chi-restraints excluded: chain I residue 29 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 I residue 97 TYR 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 51 optimal weight: 0.8980 chunk 70 optimal weight: 0.9980 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 0.0470 chunk 38 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 0.0980 chunk 76 optimal weight: 0.3980 chunk 79 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 44 optimal weight: 0.2980 overall best weight: 0.3078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 501 ASN I 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3895 r_free = 0.3895 target = 0.143573 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.110891 restraints weight = 12456.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.114539 restraints weight = 8001.575| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.116973 restraints weight = 6033.725| |-----------------------------------------------------------------------------| r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.4492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6922 Z= 0.174 Angle : 0.692 10.735 9398 Z= 0.343 Chirality : 0.044 0.224 1006 Planarity : 0.004 0.055 1199 Dihedral : 5.444 48.929 1014 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.80 % Allowed : 26.34 % Favored : 68.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.79 (0.29), residues: 847 helix: -4.45 (1.06), residues: 14 sheet: -0.05 (0.29), residues: 335 loop : -1.99 (0.27), residues: 498 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 50 HIS 0.003 0.001 HIS L 33 PHE 0.018 0.001 PHE I 100 TYR 0.020 0.001 TYR I 42 ARG 0.006 0.001 ARG L 76 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2753.66 seconds wall clock time: 48 minutes 22.15 seconds (2902.15 seconds total)