Starting phenix.real_space_refine on Fri Dec 27 22:08:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wp6_32676/12_2024/7wp6_32676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp6_32676/12_2024/7wp6_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_32676/12_2024/7wp6_32676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp6_32676/12_2024/7wp6_32676.map" model { file = "/net/cci-nas-00/data/ceres_data/7wp6_32676/12_2024/7wp6_32676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp6_32676/12_2024/7wp6_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/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: 5.31, per 1000 atoms: 0.79 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: 1.71 Conformation dependent library (CDL) restraints added in 995.4 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: 0.89 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: 1.80 Time building geometry restraints manager: 1.98 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: 4.630 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: 0.310 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 19.860 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 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:2.690 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.930 ------------------------------------------------------------------------------- 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 : 0.815 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: 0.2258 time to fit residues: 70.8299 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 : 1.014 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7742 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 12.367 9398 Z= 0.350 Chirality : 0.045 0.215 1006 Planarity : 0.005 0.059 1199 Dihedral : 6.271 41.934 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 : 0.783 Fit side-chains revert: symmetry clash REVERT: B 80 TYR cc_start: 0.7741 (m-80) cc_final: 0.7357 (m-80) REVERT: B 89 GLU cc_start: 0.7469 (mp0) cc_final: 0.7210 (mp0) REVERT: C 18 ARG cc_start: 0.4552 (OUTLIER) cc_final: 0.3749 (ttp-110) REVERT: C 54 ARG cc_start: 0.7791 (ptp90) cc_final: 0.7562 (ptp90) REVERT: D 60 TYR cc_start: 0.8863 (m-10) cc_final: 0.8461 (m-80) REVERT: D 80 TYR cc_start: 0.7884 (m-80) cc_final: 0.7575 (m-10) REVERT: F 414 GLN cc_start: 0.7433 (tt0) cc_final: 0.7038 (mp10) REVERT: H 38 LYS cc_start: 0.8921 (ttmm) cc_final: 0.8359 (ttmm) REVERT: I 41 TRP cc_start: 0.8554 (m100) cc_final: 0.8278 (m100) REVERT: I 56 TRP cc_start: 0.7159 (m100) cc_final: 0.6133 (m100) REVERT: L 38 LYS cc_start: 0.9185 (tppp) cc_final: 0.8659 (ttpt) outliers start: 26 outliers final: 20 residues processed: 222 average time/residue: 0.2159 time to fit residues: 61.0781 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 : 0.820 ------------------------------------------------------------------------------- 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 41 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 chunk 61 optimal weight: 0.2980 chunk 50 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 74 optimal weight: 1.9990 chunk 80 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 73 optimal weight: 0.0060 chunk 25 optimal weight: 0.8980 chunk 59 optimal weight: 0.5980 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 96 GLN L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7713 moved from start: 0.2902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 6922 Z= 0.190 Angle : 0.656 13.492 9398 Z= 0.330 Chirality : 0.044 0.190 1006 Planarity : 0.005 0.056 1199 Dihedral : 5.855 41.492 1015 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.12 % Allowed : 5.79 % Favored : 94.10 % Rotamer: Outliers : 5.08 % Allowed : 21.40 % Favored : 73.53 % 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: -2.63 (0.27), residues: 847 helix: -5.18 (0.46), residues: 8 sheet: -0.71 (0.27), residues: 361 loop : -2.63 (0.26), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP I 56 HIS 0.003 0.001 HIS L 33 PHE 0.022 0.001 PHE I 100 TYR 0.021 0.002 TYR I 42 ARG 0.004 0.000 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 235 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 198 time to evaluate : 0.801 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 89 GLU cc_start: 0.7550 (mp0) cc_final: 0.7211 (mp0) REVERT: C 18 ARG cc_start: 0.4638 (OUTLIER) cc_final: 0.3797 (ttp-110) REVERT: C 54 ARG cc_start: 0.7803 (ptp90) cc_final: 0.7513 (ptp90) REVERT: D 60 TYR cc_start: 0.8884 (m-10) cc_final: 0.8633 (m-80) REVERT: D 80 TYR cc_start: 0.7877 (m-80) cc_final: 0.7654 (m-10) REVERT: F 414 GLN cc_start: 0.7368 (tt0) cc_final: 0.7012 (mp10) REVERT: H 38 LYS cc_start: 0.8944 (ttmm) cc_final: 0.8633 (ttmm) REVERT: I 41 TRP cc_start: 0.8529 (m100) cc_final: 0.8307 (m100) REVERT: I 95 GLN cc_start: 0.6630 (OUTLIER) cc_final: 0.6422 (tm-30) REVERT: L 21 MET cc_start: 0.7069 (ptp) cc_final: 0.6733 (mtm) REVERT: L 38 LYS cc_start: 0.9184 (tppp) cc_final: 0.8631 (ttpt) outliers start: 37 outliers final: 26 residues processed: 215 average time/residue: 0.2017 time to fit residues: 55.8412 Evaluate side-chains 216 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 188 time to evaluate : 0.820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 GLN Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain 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 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 55 TYR Chi-restraints excluded: chain I residue 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 50 THR 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 73 optimal weight: 7.9990 chunk 56 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 8 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 2.9990 chunk 79 optimal weight: 0.7980 chunk 39 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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** H 101 HIS ** I 27 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 37 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.3054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 6922 Z= 0.450 Angle : 0.773 13.707 9398 Z= 0.391 Chirality : 0.045 0.244 1006 Planarity : 0.005 0.058 1199 Dihedral : 6.575 59.937 1015 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.12 % Allowed : 9.09 % Favored : 90.79 % Rotamer: Outliers : 7.82 % Allowed : 20.58 % Favored : 71.60 % 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: -2.64 (0.28), residues: 847 helix: -5.15 (0.51), residues: 8 sheet: -0.64 (0.28), residues: 343 loop : -2.64 (0.25), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP I 56 HIS 0.006 0.002 HIS L 33 PHE 0.026 0.002 PHE I 100 TYR 0.031 0.003 TYR I 97 ARG 0.003 0.001 ARG B 98 *********************** 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 254 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 57 poor density : 197 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8218 (m) cc_final: 0.7857 (p) REVERT: B 63 LYS cc_start: 0.9320 (tttm) cc_final: 0.8971 (tttm) REVERT: B 89 GLU cc_start: 0.7563 (mp0) cc_final: 0.7159 (mp0) REVERT: C 18 ARG cc_start: 0.5047 (OUTLIER) cc_final: 0.4669 (ttp-110) REVERT: C 54 ARG cc_start: 0.7924 (ptp90) cc_final: 0.7636 (ptp90) REVERT: D 10 GLU cc_start: 0.7287 (tm-30) cc_final: 0.6261 (tm-30) REVERT: D 60 TYR cc_start: 0.8908 (m-10) cc_final: 0.8547 (m-10) REVERT: D 80 TYR cc_start: 0.7949 (m-80) cc_final: 0.7612 (m-10) REVERT: D 102 TYR cc_start: 0.8734 (OUTLIER) cc_final: 0.8476 (p90) REVERT: F 414 GLN cc_start: 0.7527 (tt0) cc_final: 0.7132 (mp10) REVERT: F 472 ILE cc_start: 0.6386 (mm) cc_final: 0.6147 (mm) REVERT: H 38 LYS cc_start: 0.9091 (OUTLIER) cc_final: 0.8618 (ttmm) REVERT: I 21 MET cc_start: 0.5965 (mmm) cc_final: 0.5622 (mmm) REVERT: I 41 TRP cc_start: 0.8546 (m100) cc_final: 0.8218 (m100) REVERT: I 51 LYS cc_start: 0.9146 (tptt) cc_final: 0.8908 (tptt) REVERT: L 38 LYS cc_start: 0.9200 (tppp) cc_final: 0.8644 (ttpt) outliers start: 57 outliers final: 38 residues processed: 224 average time/residue: 0.2302 time to fit residues: 67.1953 Evaluate side-chains 228 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 187 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 46 LEU Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain H residue 114 LEU 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 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 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 77 VAL Chi-restraints excluded: chain L residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 0.0010 chunk 44 optimal weight: 2.9990 chunk 1 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 54 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 40 optimal weight: 0.9990 chunk 71 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.7790 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.3435 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 6922 Z= 0.220 Angle : 0.678 13.148 9398 Z= 0.339 Chirality : 0.043 0.199 1006 Planarity : 0.004 0.054 1199 Dihedral : 6.156 57.957 1015 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.38 % Favored : 93.51 % Rotamer: Outliers : 5.76 % Allowed : 24.01 % Favored : 70.23 % 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: -2.44 (0.28), residues: 847 helix: -4.97 (0.63), residues: 8 sheet: -0.47 (0.28), residues: 348 loop : -2.56 (0.25), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP I 56 HIS 0.003 0.001 HIS B 35 PHE 0.025 0.002 PHE I 100 TYR 0.022 0.002 TYR F 380 ARG 0.003 0.001 ARG L 24 *********************** 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 239 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 197 time to evaluate : 0.803 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8224 (m) cc_final: 0.7888 (p) REVERT: B 63 LYS cc_start: 0.9306 (tttm) cc_final: 0.8970 (tttm) REVERT: B 89 GLU cc_start: 0.7599 (mp0) cc_final: 0.7241 (mp0) REVERT: D 10 GLU cc_start: 0.7167 (tm-30) cc_final: 0.6197 (tm-30) REVERT: D 60 TYR cc_start: 0.8887 (m-10) cc_final: 0.8368 (m-10) REVERT: D 80 TYR cc_start: 0.7911 (m-80) cc_final: 0.7604 (m-10) REVERT: F 414 GLN cc_start: 0.7406 (tt0) cc_final: 0.7053 (mp10) REVERT: F 472 ILE cc_start: 0.6162 (mm) cc_final: 0.5933 (mm) REVERT: H 38 LYS cc_start: 0.9035 (OUTLIER) cc_final: 0.8471 (ttmm) REVERT: H 89 GLU cc_start: 0.8626 (pm20) cc_final: 0.8394 (pm20) REVERT: I 34 ASN cc_start: 0.8513 (p0) cc_final: 0.8284 (p0) REVERT: I 41 TRP cc_start: 0.8443 (m100) cc_final: 0.8206 (m100) REVERT: I 97 TYR cc_start: 0.8640 (OUTLIER) cc_final: 0.7935 (p90) REVERT: L 38 LYS cc_start: 0.9177 (tppp) cc_final: 0.8663 (ttpt) outliers start: 42 outliers final: 30 residues processed: 216 average time/residue: 0.2054 time to fit residues: 57.2706 Evaluate side-chains 218 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 186 time to evaluate : 0.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 GLN 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 46 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain 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 73 ASP Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 2 ILE Chi-restraints excluded: chain I residue 23 CYS Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 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 37 GLN Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 46 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 65 optimal weight: 0.0000 chunk 36 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 41 optimal weight: 0.6980 chunk 76 optimal weight: 1.9990 overall best weight: 0.4744 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 GLN L 37 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7734 moved from start: 0.3669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 6922 Z= 0.186 Angle : 0.661 12.393 9398 Z= 0.330 Chirality : 0.043 0.170 1006 Planarity : 0.004 0.053 1199 Dihedral : 5.776 49.736 1015 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 10.46 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer: Outliers : 5.49 % Allowed : 24.97 % Favored : 69.55 % 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: -2.22 (0.28), residues: 847 helix: -4.69 (0.87), residues: 8 sheet: -0.33 (0.28), residues: 354 loop : -2.42 (0.26), residues: 485 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 50 HIS 0.004 0.001 HIS C 55 PHE 0.022 0.001 PHE I 100 TYR 0.028 0.001 TYR F 380 ARG 0.004 0.000 ARG L 24 *********************** 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 244 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 204 time to evaluate : 0.737 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8234 (m) cc_final: 0.7993 (p) REVERT: B 63 LYS cc_start: 0.9282 (tttm) cc_final: 0.8973 (tttm) REVERT: B 89 GLU cc_start: 0.7585 (mp0) cc_final: 0.7225 (mp0) REVERT: D 23 LYS cc_start: 0.8284 (tttm) cc_final: 0.7847 (ttmm) REVERT: D 80 TYR cc_start: 0.7868 (m-80) cc_final: 0.7621 (m-10) REVERT: F 414 GLN cc_start: 0.7283 (tt0) cc_final: 0.6890 (mp10) REVERT: F 472 ILE cc_start: 0.6147 (mm) cc_final: 0.5923 (mm) REVERT: H 3 GLN cc_start: 0.8356 (tt0) cc_final: 0.7914 (tm-30) REVERT: H 38 LYS cc_start: 0.8995 (OUTLIER) cc_final: 0.8542 (ttmm) REVERT: H 69 THR cc_start: 0.8980 (m) cc_final: 0.8573 (p) REVERT: I 21 MET cc_start: 0.5756 (mmm) cc_final: 0.5453 (mmm) REVERT: I 56 TRP cc_start: 0.7928 (m-10) cc_final: 0.7579 (m-10) REVERT: I 97 TYR cc_start: 0.8710 (OUTLIER) cc_final: 0.7948 (p90) REVERT: L 38 LYS cc_start: 0.9168 (tppp) cc_final: 0.8665 (ttpt) outliers start: 40 outliers final: 29 residues processed: 225 average time/residue: 0.2115 time to fit residues: 61.2436 Evaluate side-chains 224 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 193 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 GLN 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 92 SER Chi-restraints excluded: chain D residue 71 THR Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 114 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 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 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 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 8 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 44 optimal weight: 0.0670 chunk 66 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 36 optimal weight: 6.9990 chunk 31 optimal weight: 0.5980 chunk 47 optimal weight: 0.0060 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN ** D 35 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7707 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 6922 Z= 0.176 Angle : 0.667 12.702 9398 Z= 0.330 Chirality : 0.043 0.157 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.516 47.487 1015 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.79 % Favored : 94.21 % Rotamer: Outliers : 4.53 % Allowed : 26.34 % Favored : 69.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (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: -1.99 (0.28), residues: 847 helix: -4.42 (1.12), residues: 8 sheet: -0.14 (0.29), residues: 336 loop : -2.22 (0.26), residues: 503 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 436 HIS 0.003 0.001 HIS C 55 PHE 0.019 0.001 PHE I 100 TYR 0.022 0.001 TYR F 380 ARG 0.005 0.001 ARG C 54 *********************** 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 230 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 0.729 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 63 LYS cc_start: 0.9304 (tttm) cc_final: 0.8971 (tttm) REVERT: B 89 GLU cc_start: 0.7585 (mp0) cc_final: 0.7277 (mp0) REVERT: D 23 LYS cc_start: 0.8238 (tttm) cc_final: 0.7790 (ttmm) REVERT: D 60 TYR cc_start: 0.8912 (m-10) cc_final: 0.8575 (m-10) REVERT: F 414 GLN cc_start: 0.7278 (tt0) cc_final: 0.6882 (mp10) REVERT: F 472 ILE cc_start: 0.6162 (mm) cc_final: 0.5934 (mm) REVERT: H 38 LYS cc_start: 0.8973 (OUTLIER) cc_final: 0.8514 (ttmm) REVERT: I 56 TRP cc_start: 0.7725 (m-10) cc_final: 0.7497 (m-10) REVERT: I 97 TYR cc_start: 0.8600 (OUTLIER) cc_final: 0.8136 (p90) REVERT: L 38 LYS cc_start: 0.9173 (tppp) cc_final: 0.8671 (ttpt) outliers start: 33 outliers final: 24 residues processed: 215 average time/residue: 0.2062 time to fit residues: 57.3642 Evaluate side-chains 211 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 185 time to evaluate : 0.838 ------------------------------------------------------------------------------- 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 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 92 SER Chi-restraints excluded: chain D residue 114 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 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 64 VAL Chi-restraints excluded: chain I residue 67 ARG Chi-restraints excluded: chain I residue 68 PHE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 0.0020 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 62 optimal weight: 5.9990 chunk 71 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 69 optimal weight: 0.9990 chunk 73 optimal weight: 2.9990 overall best weight: 0.8592 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7757 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6922 Z= 0.233 Angle : 0.700 12.535 9398 Z= 0.345 Chirality : 0.043 0.179 1006 Planarity : 0.004 0.056 1199 Dihedral : 5.525 46.350 1015 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.97 % Favored : 92.92 % Rotamer: Outliers : 4.80 % Allowed : 26.61 % 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: -1.99 (0.28), residues: 847 helix: -4.28 (1.26), residues: 8 sheet: -0.22 (0.28), residues: 353 loop : -2.22 (0.27), residues: 486 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP F 353 HIS 0.003 0.001 HIS H 101 PHE 0.021 0.002 PHE I 100 TYR 0.022 0.002 TYR C 91 ARG 0.004 0.001 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 222 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 187 time to evaluate : 0.964 Fit side-chains revert: symmetry clash REVERT: B 63 LYS cc_start: 0.9278 (tttm) cc_final: 0.9010 (tttm) REVERT: B 89 GLU cc_start: 0.7618 (mp0) cc_final: 0.7304 (mp0) REVERT: D 23 LYS cc_start: 0.8256 (tttm) cc_final: 0.7845 (ttmm) REVERT: D 60 TYR cc_start: 0.8845 (m-10) cc_final: 0.8284 (m-80) REVERT: D 88 SER cc_start: 0.8706 (m) cc_final: 0.8491 (p) REVERT: F 414 GLN cc_start: 0.7305 (tt0) cc_final: 0.6912 (mp10) REVERT: H 38 LYS cc_start: 0.8977 (OUTLIER) cc_final: 0.8514 (ttmm) REVERT: I 21 MET cc_start: 0.5842 (mmm) cc_final: 0.5407 (mmm) REVERT: I 56 TRP cc_start: 0.7776 (m-10) cc_final: 0.7526 (m-10) REVERT: I 67 ARG cc_start: 0.6028 (OUTLIER) cc_final: 0.5552 (ptt180) REVERT: I 97 TYR cc_start: 0.8606 (OUTLIER) cc_final: 0.8019 (p90) REVERT: L 38 LYS cc_start: 0.9204 (tppp) cc_final: 0.8683 (ttpt) outliers start: 35 outliers final: 27 residues processed: 206 average time/residue: 0.2356 time to fit residues: 63.3351 Evaluate side-chains 211 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 181 time to evaluate : 0.813 ------------------------------------------------------------------------------- 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 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 D residue 71 THR Chi-restraints excluded: chain D residue 74 LYS Chi-restraints excluded: chain D residue 114 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 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 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 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 72 LEU Chi-restraints excluded: chain L residue 77 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 32 optimal weight: 0.0270 chunk 57 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 69 optimal weight: 7.9990 chunk 73 optimal weight: 6.9990 chunk 48 optimal weight: 1.9990 chunk 77 optimal weight: 4.9990 chunk 47 optimal weight: 0.9980 overall best weight: 1.4044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 35 HIS B 41 HIS H 3 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.4066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 6922 Z= 0.323 Angle : 0.753 12.509 9398 Z= 0.375 Chirality : 0.046 0.324 1006 Planarity : 0.004 0.056 1199 Dihedral : 5.849 46.882 1014 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 11.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.15 % Favored : 91.74 % Rotamer: Outliers : 4.94 % Allowed : 27.30 % Favored : 67.76 % 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: -2.00 (0.28), residues: 847 helix: -4.20 (1.34), residues: 8 sheet: -0.18 (0.29), residues: 337 loop : -2.22 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP F 353 HIS 0.004 0.001 HIS B 35 PHE 0.023 0.002 PHE I 100 TYR 0.023 0.002 TYR I 97 ARG 0.005 0.001 ARG D 99 *********************** 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 214 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 178 time to evaluate : 0.715 Fit side-chains revert: symmetry clash REVERT: B 63 LYS cc_start: 0.9333 (tttm) cc_final: 0.9024 (tttm) REVERT: B 89 GLU cc_start: 0.7669 (mp0) cc_final: 0.7330 (mp0) REVERT: D 60 TYR cc_start: 0.8870 (m-10) cc_final: 0.8347 (m-80) REVERT: F 414 GLN cc_start: 0.7410 (tt0) cc_final: 0.6980 (mp10) REVERT: H 38 LYS cc_start: 0.9034 (OUTLIER) cc_final: 0.8528 (ttmm) REVERT: H 69 THR cc_start: 0.9063 (m) cc_final: 0.8626 (p) REVERT: I 21 MET cc_start: 0.5847 (mmm) cc_final: 0.5441 (mmm) REVERT: I 51 LYS cc_start: 0.8989 (tptt) cc_final: 0.8788 (tptt) REVERT: I 97 TYR cc_start: 0.8573 (OUTLIER) cc_final: 0.7891 (p90) REVERT: L 38 LYS cc_start: 0.9216 (tppp) cc_final: 0.8697 (ttpt) outliers start: 36 outliers final: 28 residues processed: 196 average time/residue: 0.2142 time to fit residues: 53.5541 Evaluate side-chains 207 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 177 time to evaluate : 0.793 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 19 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 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 D residue 71 THR Chi-restraints excluded: chain D residue 102 TYR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 380 TYR Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 86 LEU Chi-restraints excluded: chain H residue 107 PHE Chi-restraints excluded: chain H residue 112 THR Chi-restraints excluded: chain I residue 29 LEU Chi-restraints excluded: chain I residue 42 TYR Chi-restraints excluded: chain I residue 64 VAL 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 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 2.9990 chunk 54 optimal weight: 2.9990 chunk 81 optimal weight: 0.5980 chunk 75 optimal weight: 0.8980 chunk 65 optimal weight: 0.0470 chunk 6 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 39 optimal weight: 0.4980 chunk 51 optimal weight: 3.9990 chunk 69 optimal weight: 0.0970 chunk 19 optimal weight: 0.8980 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN H 39 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.4276 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= 0.186 Angle : 0.706 11.778 9398 Z= 0.349 Chirality : 0.044 0.259 1006 Planarity : 0.004 0.055 1199 Dihedral : 5.551 49.495 1014 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 4.25 % Allowed : 27.57 % Favored : 68.18 % 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: -3.97 (1.55), residues: 8 sheet: -0.06 (0.28), residues: 339 loop : -2.19 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 50 HIS 0.003 0.001 HIS C 55 PHE 0.019 0.001 PHE I 100 TYR 0.020 0.002 TYR I 42 ARG 0.010 0.001 ARG L 76 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1694 Ramachandran restraints generated. 847 Oldfield, 0 Emsley, 847 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 190 time to evaluate : 0.694 Fit side-chains revert: symmetry clash REVERT: B 89 GLU cc_start: 0.7663 (mp0) cc_final: 0.7336 (mp0) REVERT: D 10 GLU cc_start: 0.7120 (tm-30) cc_final: 0.6433 (tm-30) REVERT: D 23 LYS cc_start: 0.8191 (tttm) cc_final: 0.7739 (ttmm) REVERT: D 60 TYR cc_start: 0.8885 (m-10) cc_final: 0.8359 (m-80) REVERT: D 80 TYR cc_start: 0.7814 (m-80) cc_final: 0.7478 (m-10) REVERT: F 414 GLN cc_start: 0.7244 (tt0) cc_final: 0.6973 (mp10) REVERT: F 516 GLU cc_start: 0.7123 (tt0) cc_final: 0.6617 (tm-30) REVERT: H 38 LYS cc_start: 0.8996 (OUTLIER) cc_final: 0.8583 (ttmm) REVERT: H 80 TYR cc_start: 0.8010 (m-80) cc_final: 0.7780 (m-80) REVERT: I 21 MET cc_start: 0.5773 (mmm) cc_final: 0.5408 (mmm) REVERT: I 67 ARG cc_start: 0.6242 (OUTLIER) cc_final: 0.5816 (ptt180) REVERT: I 97 TYR cc_start: 0.8516 (OUTLIER) cc_final: 0.8026 (p90) REVERT: L 38 LYS cc_start: 0.9218 (tppp) cc_final: 0.8688 (ttpt) REVERT: L 76 ARG cc_start: 0.7821 (mmt-90) cc_final: 0.7538 (mmp80) outliers start: 31 outliers final: 26 residues processed: 203 average time/residue: 0.2182 time to fit residues: 56.7925 Evaluate side-chains 212 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 183 time to evaluate : 1.011 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 48 ILE Chi-restraints excluded: chain B residue 118 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 D residue 71 THR Chi-restraints excluded: chain D residue 114 THR Chi-restraints excluded: chain D residue 117 THR Chi-restraints excluded: chain F residue 368 LEU Chi-restraints excluded: chain F residue 478 THR Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 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 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 77 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 66 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 57 optimal weight: 0.0470 chunk 3 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 overall best weight: 1.1282 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.138937 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.105917 restraints weight = 12166.736| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109427 restraints weight = 7843.813| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.111869 restraints weight = 5954.906| |-----------------------------------------------------------------------------| r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7801 moved from start: 0.4335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 6922 Z= 0.277 Angle : 0.736 11.671 9398 Z= 0.367 Chirality : 0.045 0.243 1006 Planarity : 0.004 0.056 1199 Dihedral : 5.763 49.550 1014 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.12 % Allowed : 8.26 % Favored : 91.62 % Rotamer: Outliers : 4.39 % Allowed : 27.71 % Favored : 67.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (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: -1.92 (0.28), residues: 847 helix: -3.92 (1.61), residues: 8 sheet: -0.12 (0.28), residues: 334 loop : -2.16 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 353 HIS 0.003 0.001 HIS C 55 PHE 0.021 0.002 PHE I 100 TYR 0.023 0.002 TYR D 32 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: 2095.16 seconds wall clock time: 38 minutes 59.25 seconds (2339.25 seconds total)