Starting phenix.real_space_refine on Thu Jun 5 22:42:17 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wp6_32676/06_2025/7wp6_32676.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wp6_32676/06_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_32676/06_2025/7wp6_32676.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wp6_32676/06_2025/7wp6_32676.map" model { file = "/net/cci-nas-00/data/ceres_data/7wp6_32676/06_2025/7wp6_32676.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wp6_32676/06_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-5710/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: 6.25, per 1000 atoms: 0.93 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: 1.48 Conformation dependent library (CDL) restraints added in 906.5 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: 0.90 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: 1.70 Time building geometry restraints manager: 1.80 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: 4.250 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: 0.060 Process input model: 20.260 Find NCS groups from input model: 0.110 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.620 ------------------------------------------------------------------------------- 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 : 0.011 0.684 6932 Z= 0.547 Angle : 1.138 32.640 9421 Z= 0.621 Chirality : 0.062 0.397 1006 Planarity : 0.013 0.284 1199 Dihedral : 14.824 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00701 ( 2) link_NAG-ASN : angle 2.08832 ( 6) link_BETA1-4 : bond 0.01095 ( 1) link_BETA1-4 : angle 6.88447 ( 3) hydrogen bonds : bond 0.28652 ( 154) hydrogen bonds : angle 11.18493 ( 402) SS BOND : bond 0.25876 ( 7) SS BOND : angle 9.81092 ( 14) covalent geometry : bond 0.00768 ( 6922) covalent geometry : angle 1.06603 ( 9398) *********************** 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 : 0.814 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: 0.2251 time to fit residues: 70.4338 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 : 0.748 ------------------------------------------------------------------------------- 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: 4.9990 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 6932 Z= 0.151 Angle : 0.694 12.368 9421 Z= 0.352 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 2) link_NAG-ASN : angle 2.08377 ( 6) link_BETA1-4 : bond 0.01037 ( 1) link_BETA1-4 : angle 5.72330 ( 3) hydrogen bonds : bond 0.04524 ( 154) hydrogen bonds : angle 7.78685 ( 402) SS BOND : bond 0.00635 ( 7) SS BOND : angle 1.49907 ( 14) covalent geometry : bond 0.00340 ( 6922) covalent geometry : angle 0.68318 ( 9398) *********************** 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 : 0.703 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: 0.2103 time to fit residues: 59.4649 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 : 0.797 ------------------------------------------------------------------------------- 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: 2.9990 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 6932 Z= 0.236 Angle : 0.743 13.940 9421 Z= 0.374 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 Details of bonding type rmsd link_NAG-ASN : bond 0.00099 ( 2) link_NAG-ASN : angle 1.46112 ( 6) link_BETA1-4 : bond 0.01207 ( 1) link_BETA1-4 : angle 5.25443 ( 3) hydrogen bonds : bond 0.04310 ( 154) hydrogen bonds : angle 7.21978 ( 402) SS BOND : bond 0.00557 ( 7) SS BOND : angle 1.73745 ( 14) covalent geometry : bond 0.00542 ( 6922) covalent geometry : angle 0.73401 ( 9398) *********************** 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 : 0.730 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: 0.2089 time to fit residues: 58.9923 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 : 0.842 ------------------------------------------------------------------------------- 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: 2.9990 chunk 48 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 51 optimal weight: 7.9990 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 = 0.3818 r_free = 0.3818 target = 0.137252 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.104635 restraints weight = 12620.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.108235 restraints weight = 7963.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.110675 restraints weight = 5978.048| |-----------------------------------------------------------------------------| r_work (final): 0.3478 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 6932 Z= 0.182 Angle : 0.700 13.458 9421 Z= 0.350 Chirality : 0.044 0.220 1006 Planarity : 0.004 0.054 1199 Dihedral : 6.252 54.549 1015 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 12.28 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.44 % Favored : 92.44 % Rotamer: Outliers : 6.04 % Allowed : 22.63 % Favored : 71.33 % 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: -2.54 (0.28), residues: 847 helix: -5.13 (0.51), residues: 8 sheet: -0.58 (0.28), residues: 345 loop : -2.58 (0.25), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP I 56 HIS 0.004 0.001 HIS L 33 PHE 0.026 0.002 PHE I 100 TYR 0.021 0.002 TYR I 42 ARG 0.004 0.001 ARG L 24 Details of bonding type rmsd link_NAG-ASN : bond 0.00082 ( 2) link_NAG-ASN : angle 1.42622 ( 6) link_BETA1-4 : bond 0.01082 ( 1) link_BETA1-4 : angle 5.19619 ( 3) hydrogen bonds : bond 0.03673 ( 154) hydrogen bonds : angle 6.75614 ( 402) SS BOND : bond 0.00452 ( 7) SS BOND : angle 1.34936 ( 14) covalent geometry : bond 0.00421 ( 6922) covalent geometry : angle 0.69224 ( 9398) *********************** 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 239 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 195 time to evaluate : 0.812 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8258 (m) cc_final: 0.7819 (p) REVERT: B 63 LYS cc_start: 0.9301 (tttm) cc_final: 0.8874 (tttp) REVERT: B 89 GLU cc_start: 0.7606 (mp0) cc_final: 0.7223 (mp0) REVERT: C 18 ARG cc_start: 0.5653 (OUTLIER) cc_final: 0.4866 (ttp-110) REVERT: D 60 TYR cc_start: 0.8862 (m-10) cc_final: 0.8430 (m-80) REVERT: D 80 TYR cc_start: 0.7854 (m-80) cc_final: 0.7635 (m-10) REVERT: F 414 GLN cc_start: 0.7387 (tt0) cc_final: 0.7137 (mp10) REVERT: F 472 ILE cc_start: 0.6283 (mm) cc_final: 0.6053 (mm) REVERT: H 38 LYS cc_start: 0.9011 (OUTLIER) cc_final: 0.8466 (ttmm) REVERT: I 21 MET cc_start: 0.5860 (mmm) cc_final: 0.5566 (mmm) REVERT: I 36 LYS cc_start: 0.7013 (mtpt) cc_final: 0.6757 (mtpt) REVERT: I 41 TRP cc_start: 0.8524 (m100) cc_final: 0.8253 (m100) REVERT: I 97 TYR cc_start: 0.8639 (OUTLIER) cc_final: 0.7890 (p90) REVERT: L 38 LYS cc_start: 0.9204 (tppp) cc_final: 0.8658 (ttpt) outliers start: 44 outliers final: 32 residues processed: 216 average time/residue: 0.2004 time to fit residues: 56.0134 Evaluate side-chains 219 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 184 time to evaluate : 0.757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 18 ARG Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 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 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 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: 2.9990 chunk 13 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 57 optimal weight: 0.3980 chunk 32 optimal weight: 0.8980 chunk 45 optimal weight: 2.9990 chunk 50 optimal weight: 5.9990 chunk 48 optimal weight: 0.7980 chunk 21 optimal weight: 0.2980 chunk 58 optimal weight: 0.9990 chunk 8 optimal weight: 6.9990 overall best weight: 0.6782 ------------------------------------------------------------------------------- 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 = 0.3839 r_free = 0.3839 target = 0.138819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.106465 restraints weight = 12239.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3448 r_free = 0.3448 target = 0.110068 restraints weight = 7767.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.112615 restraints weight = 5801.399| |-----------------------------------------------------------------------------| r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.3440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6932 Z= 0.136 Angle : 0.680 13.380 9421 Z= 0.336 Chirality : 0.043 0.191 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.966 52.384 1015 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.61 % Favored : 93.27 % Rotamer: Outliers : 5.76 % Allowed : 24.42 % Favored : 69.82 % 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: -2.39 (0.28), residues: 847 helix: -4.89 (0.70), residues: 8 sheet: -0.50 (0.28), residues: 351 loop : -2.47 (0.26), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP I 56 HIS 0.002 0.001 HIS B 35 PHE 0.024 0.001 PHE I 100 TYR 0.024 0.002 TYR F 380 ARG 0.003 0.000 ARG H 40 Details of bonding type rmsd link_NAG-ASN : bond 0.00059 ( 2) link_NAG-ASN : angle 1.32330 ( 6) link_BETA1-4 : bond 0.01162 ( 1) link_BETA1-4 : angle 5.11433 ( 3) hydrogen bonds : bond 0.03421 ( 154) hydrogen bonds : angle 6.31746 ( 402) SS BOND : bond 0.00659 ( 7) SS BOND : angle 1.82690 ( 14) covalent geometry : bond 0.00315 ( 6922) covalent geometry : angle 0.66974 ( 9398) *********************** 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 237 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 195 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8265 (m) cc_final: 0.7850 (p) REVERT: B 63 LYS cc_start: 0.9298 (tttm) cc_final: 0.9007 (tttm) REVERT: B 89 GLU cc_start: 0.7617 (mp0) cc_final: 0.7265 (mp0) REVERT: D 23 LYS cc_start: 0.8202 (tttm) cc_final: 0.7811 (ttmm) REVERT: D 80 TYR cc_start: 0.7908 (m-80) cc_final: 0.7690 (m-10) REVERT: F 414 GLN cc_start: 0.7306 (tt0) cc_final: 0.7075 (mp10) REVERT: F 472 ILE cc_start: 0.6284 (mm) cc_final: 0.6038 (mm) REVERT: H 3 GLN cc_start: 0.8359 (tt0) cc_final: 0.7918 (tm-30) REVERT: H 38 LYS cc_start: 0.8997 (OUTLIER) cc_final: 0.8471 (ttmm) REVERT: I 56 TRP cc_start: 0.7885 (m-10) cc_final: 0.7570 (m-10) REVERT: L 38 LYS cc_start: 0.9202 (tppp) cc_final: 0.8690 (ttpt) outliers start: 42 outliers final: 33 residues processed: 217 average time/residue: 0.1998 time to fit residues: 56.5073 Evaluate side-chains 221 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 187 time to evaluate : 0.964 ------------------------------------------------------------------------------- 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 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 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 95 GLN 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 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 48 optimal weight: 2.9990 chunk 43 optimal weight: 0.0020 chunk 49 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 67 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 55 optimal weight: 0.3980 chunk 74 optimal weight: 1.9990 chunk 52 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 32 optimal weight: 0.0370 overall best weight: 0.4466 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.141251 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.108674 restraints weight = 12253.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3479 r_free = 0.3479 target = 0.112248 restraints weight = 7797.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.114774 restraints weight = 5858.018| |-----------------------------------------------------------------------------| r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6932 Z= 0.115 Angle : 0.656 12.446 9421 Z= 0.323 Chirality : 0.043 0.161 1006 Planarity : 0.004 0.053 1199 Dihedral : 5.682 48.676 1015 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 5.21 % Allowed : 25.93 % 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: -2.09 (0.28), residues: 847 helix: -4.53 (1.02), residues: 8 sheet: -0.24 (0.28), residues: 348 loop : -2.32 (0.26), residues: 491 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP I 56 HIS 0.002 0.001 HIS B 35 PHE 0.021 0.001 PHE I 100 TYR 0.022 0.001 TYR F 380 ARG 0.005 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00078 ( 2) link_NAG-ASN : angle 1.29359 ( 6) link_BETA1-4 : bond 0.01155 ( 1) link_BETA1-4 : angle 4.93446 ( 3) hydrogen bonds : bond 0.03130 ( 154) hydrogen bonds : angle 5.97668 ( 402) SS BOND : bond 0.00610 ( 7) SS BOND : angle 1.32689 ( 14) covalent geometry : bond 0.00268 ( 6922) covalent geometry : angle 0.64829 ( 9398) *********************** 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: 38 poor density : 197 time to evaluate : 0.736 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8170 (m) cc_final: 0.7841 (p) REVERT: B 63 LYS cc_start: 0.9310 (tttm) cc_final: 0.8931 (tttm) REVERT: B 89 GLU cc_start: 0.7568 (mp0) cc_final: 0.7256 (mp0) REVERT: D 23 LYS cc_start: 0.8222 (tttm) cc_final: 0.7831 (ttmm) REVERT: F 414 GLN cc_start: 0.7242 (tt0) cc_final: 0.6924 (mp10) REVERT: F 472 ILE cc_start: 0.6173 (mm) cc_final: 0.5969 (mm) REVERT: H 3 GLN cc_start: 0.8383 (tt0) cc_final: 0.7921 (tm-30) REVERT: H 38 LYS cc_start: 0.8985 (OUTLIER) cc_final: 0.8480 (ttmm) REVERT: L 38 LYS cc_start: 0.9184 (tppp) cc_final: 0.8650 (ttpt) outliers start: 38 outliers final: 31 residues processed: 214 average time/residue: 0.1974 time to fit residues: 54.7583 Evaluate side-chains 221 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 189 time to evaluate : 0.721 ------------------------------------------------------------------------------- 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 48 ILE Chi-restraints excluded: chain B residue 87 THR Chi-restraints excluded: chain B residue 118 VAL Chi-restraints excluded: chain C residue 3 VAL Chi-restraints excluded: chain C residue 27 GLN Chi-restraints excluded: chain C residue 75 ILE Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 81 GLU Chi-restraints excluded: chain C residue 92 SER Chi-restraints excluded: chain D residue 102 TYR 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 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 L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 37 GLN Chi-restraints excluded: chain L residue 50 THR Chi-restraints excluded: chain L residue 68 THR Chi-restraints excluded: chain L residue 72 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 33 optimal weight: 0.3980 chunk 70 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 80 optimal weight: 0.5980 chunk 72 optimal weight: 0.8980 chunk 73 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 12 optimal weight: 5.9990 chunk 45 optimal weight: 0.0070 chunk 64 optimal weight: 0.6980 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 20 ASN H 101 HIS I 27 GLN I 34 ASN L 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.141603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109008 restraints weight = 12045.550| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.112734 restraints weight = 7500.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.115268 restraints weight = 5550.820| |-----------------------------------------------------------------------------| r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 0.3944 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6932 Z= 0.122 Angle : 0.667 12.106 9421 Z= 0.328 Chirality : 0.043 0.159 1006 Planarity : 0.004 0.055 1199 Dihedral : 5.585 48.182 1015 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.49 % Favored : 93.39 % Rotamer: Outliers : 6.04 % Allowed : 25.79 % 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: -1.95 (0.28), residues: 847 helix: -4.41 (1.13), residues: 8 sheet: -0.11 (0.29), residues: 327 loop : -2.17 (0.26), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP I 56 HIS 0.003 0.001 HIS H 101 PHE 0.019 0.001 PHE I 100 TYR 0.021 0.001 TYR I 42 ARG 0.004 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00069 ( 2) link_NAG-ASN : angle 1.27504 ( 6) link_BETA1-4 : bond 0.01125 ( 1) link_BETA1-4 : angle 4.78781 ( 3) hydrogen bonds : bond 0.03110 ( 154) hydrogen bonds : angle 5.83064 ( 402) SS BOND : bond 0.00567 ( 7) SS BOND : angle 1.46205 ( 14) covalent geometry : bond 0.00284 ( 6922) covalent geometry : angle 0.65905 ( 9398) *********************** 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 241 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 197 time to evaluate : 0.784 Fit side-chains revert: symmetry clash REVERT: B 17 SER cc_start: 0.8205 (m) cc_final: 0.7964 (p) REVERT: B 54 ASN cc_start: 0.8870 (t0) cc_final: 0.8655 (m-40) REVERT: B 63 LYS cc_start: 0.9255 (tttm) cc_final: 0.8979 (tttm) REVERT: B 89 GLU cc_start: 0.7595 (mp0) cc_final: 0.7258 (mp0) REVERT: D 10 GLU cc_start: 0.7116 (tm-30) cc_final: 0.6252 (tm-30) REVERT: D 23 LYS cc_start: 0.8251 (tttm) cc_final: 0.7866 (ttmm) REVERT: F 414 GLN cc_start: 0.7187 (tt0) cc_final: 0.6950 (mp10) REVERT: F 472 ILE cc_start: 0.6234 (mm) cc_final: 0.6025 (mm) REVERT: H 38 LYS cc_start: 0.8963 (OUTLIER) cc_final: 0.8481 (ttmm) REVERT: H 69 THR cc_start: 0.8950 (m) cc_final: 0.8513 (p) REVERT: I 21 MET cc_start: 0.5777 (mmm) cc_final: 0.5322 (mmm) REVERT: I 97 TYR cc_start: 0.8677 (OUTLIER) cc_final: 0.8052 (p90) REVERT: L 38 LYS cc_start: 0.9203 (tppp) cc_final: 0.8654 (ttpt) outliers start: 44 outliers final: 31 residues processed: 219 average time/residue: 0.2046 time to fit residues: 58.0247 Evaluate side-chains 220 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 187 time to evaluate : 0.685 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 5 GLN 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 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 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 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 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: 0.6980 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 chunk 65 optimal weight: 0.0570 chunk 59 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 26 optimal weight: 1.9990 chunk 58 optimal weight: 0.8980 overall best weight: 0.5698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN I 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3876 r_free = 0.3876 target = 0.141758 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3432 r_free = 0.3432 target = 0.108852 restraints weight = 12363.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.112599 restraints weight = 7793.641| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3520 r_free = 0.3520 target = 0.115156 restraints weight = 5800.444| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6932 Z= 0.125 Angle : 0.682 11.684 9421 Z= 0.336 Chirality : 0.044 0.329 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.555 47.905 1015 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.40 Ramachandran Plot: Outliers : 0.12 % Allowed : 6.14 % Favored : 93.74 % Rotamer: Outliers : 5.49 % Allowed : 25.51 % 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: -1.91 (0.28), residues: 847 helix: -4.36 (1.19), residues: 8 sheet: -0.09 (0.29), residues: 331 loop : -2.15 (0.26), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 36 HIS 0.003 0.001 HIS H 101 PHE 0.019 0.001 PHE I 100 TYR 0.020 0.001 TYR I 42 ARG 0.004 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00073 ( 2) link_NAG-ASN : angle 1.27129 ( 6) link_BETA1-4 : bond 0.01008 ( 1) link_BETA1-4 : angle 4.66418 ( 3) hydrogen bonds : bond 0.03036 ( 154) hydrogen bonds : angle 5.71601 ( 402) SS BOND : bond 0.00533 ( 7) SS BOND : angle 1.25645 ( 14) covalent geometry : bond 0.00293 ( 6922) covalent geometry : angle 0.67480 ( 9398) *********************** 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 228 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 188 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 17 SER cc_start: 0.8292 (m) cc_final: 0.8055 (p) REVERT: B 89 GLU cc_start: 0.7589 (mp0) cc_final: 0.7274 (mp0) REVERT: C 54 ARG cc_start: 0.7773 (ptp90) cc_final: 0.7256 (ptp90) REVERT: D 10 GLU cc_start: 0.7230 (tm-30) cc_final: 0.6369 (tm-30) REVERT: D 23 LYS cc_start: 0.8270 (tttm) cc_final: 0.7843 (ttmm) REVERT: F 414 GLN cc_start: 0.7200 (tt0) cc_final: 0.6982 (mp10) REVERT: H 38 LYS cc_start: 0.8959 (OUTLIER) cc_final: 0.8502 (ttmm) REVERT: I 21 MET cc_start: 0.5816 (mmm) cc_final: 0.5479 (mmm) REVERT: I 97 TYR cc_start: 0.8641 (OUTLIER) cc_final: 0.7964 (p90) REVERT: L 38 LYS cc_start: 0.9205 (tppp) cc_final: 0.8663 (ttpt) REVERT: L 76 ARG cc_start: 0.8215 (tmm160) cc_final: 0.7874 (tmm160) REVERT: L 78 GLU cc_start: 0.8399 (tt0) cc_final: 0.8069 (tt0) outliers start: 40 outliers final: 32 residues processed: 207 average time/residue: 0.2169 time to fit residues: 58.2798 Evaluate side-chains 217 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.799 ------------------------------------------------------------------------------- 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 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 F residue 503 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 38 LYS Chi-restraints excluded: chain H residue 101 HIS 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 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 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 7 optimal weight: 4.9990 chunk 73 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 65 optimal weight: 0.9980 chunk 35 optimal weight: 0.0870 chunk 37 optimal weight: 3.9990 chunk 63 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 41 optimal weight: 2.9990 chunk 74 optimal weight: 2.9990 chunk 46 optimal weight: 0.0170 overall best weight: 0.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 41 HIS 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 = 0.3829 r_free = 0.3829 target = 0.138583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.105224 restraints weight = 12465.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.108810 restraints weight = 7929.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3460 r_free = 0.3460 target = 0.111249 restraints weight = 5975.679| |-----------------------------------------------------------------------------| r_work (final): 0.3459 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6932 Z= 0.163 Angle : 0.710 11.561 9421 Z= 0.352 Chirality : 0.044 0.241 1006 Planarity : 0.004 0.056 1199 Dihedral : 5.755 49.530 1015 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.79 % Favored : 92.09 % 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: -1.93 (0.28), residues: 847 helix: -4.23 (1.31), residues: 8 sheet: -0.23 (0.28), residues: 343 loop : -2.09 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 353 HIS 0.004 0.001 HIS H 101 PHE 0.020 0.002 PHE I 100 TYR 0.025 0.002 TYR C 91 ARG 0.003 0.000 ARG C 54 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 2) link_NAG-ASN : angle 1.32972 ( 6) link_BETA1-4 : bond 0.01045 ( 1) link_BETA1-4 : angle 4.47907 ( 3) hydrogen bonds : bond 0.03166 ( 154) hydrogen bonds : angle 5.81352 ( 402) SS BOND : bond 0.00516 ( 7) SS BOND : angle 1.16967 ( 14) covalent geometry : bond 0.00381 ( 6922) covalent geometry : angle 0.70442 ( 9398) *********************** 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 223 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 187 time to evaluate : 0.728 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 54 ASN cc_start: 0.8979 (t0) cc_final: 0.8764 (m-40) REVERT: B 89 GLU cc_start: 0.7634 (mp0) cc_final: 0.7302 (mp0) REVERT: C 54 ARG cc_start: 0.7816 (ptp90) cc_final: 0.7328 (ptp90) REVERT: D 10 GLU cc_start: 0.7241 (tm-30) cc_final: 0.6417 (tm-30) REVERT: D 23 LYS cc_start: 0.8311 (tttm) cc_final: 0.7917 (ttmm) REVERT: F 414 GLN cc_start: 0.7287 (tt0) cc_final: 0.7003 (mp10) REVERT: H 38 LYS cc_start: 0.8971 (OUTLIER) cc_final: 0.8514 (ttmm) REVERT: I 21 MET cc_start: 0.5855 (mmm) cc_final: 0.5539 (mmm) REVERT: I 97 TYR cc_start: 0.8727 (OUTLIER) cc_final: 0.8114 (p90) REVERT: L 38 LYS cc_start: 0.9222 (tppp) cc_final: 0.8678 (ttpt) REVERT: L 76 ARG cc_start: 0.8250 (tmm160) cc_final: 0.7888 (tmm160) REVERT: L 78 GLU cc_start: 0.8429 (tt0) cc_final: 0.8026 (tt0) outliers start: 36 outliers final: 31 residues processed: 204 average time/residue: 0.2011 time to fit residues: 52.8757 Evaluate side-chains 213 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 180 time to evaluate : 0.731 ------------------------------------------------------------------------------- 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 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 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 101 HIS 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 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 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 74 optimal weight: 4.9990 chunk 66 optimal weight: 0.2980 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 53 optimal weight: 1.9990 chunk 49 optimal weight: 0.0000 chunk 17 optimal weight: 3.9990 chunk 63 optimal weight: 7.9990 chunk 21 optimal weight: 0.1980 chunk 2 optimal weight: 0.4980 chunk 11 optimal weight: 4.9990 overall best weight: 0.3384 ------------------------------------------------------------------------------- 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** H 3 GLN H 39 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 = 0.3913 r_free = 0.3913 target = 0.143663 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.111720 restraints weight = 12517.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.115459 restraints weight = 7915.495| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3567 r_free = 0.3567 target = 0.117936 restraints weight = 5886.965| |-----------------------------------------------------------------------------| r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7696 moved from start: 0.4395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6932 Z= 0.116 Angle : 0.697 10.885 9421 Z= 0.344 Chirality : 0.044 0.230 1006 Planarity : 0.004 0.054 1199 Dihedral : 5.528 47.596 1015 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 10.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.31 % Favored : 94.69 % Rotamer: Outliers : 5.08 % Allowed : 26.61 % Favored : 68.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.12 % Rama-Z (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: -1.81 (0.28), residues: 847 helix: -3.97 (1.57), residues: 8 sheet: -0.07 (0.28), residues: 337 loop : -2.07 (0.26), residues: 502 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP I 41 HIS 0.002 0.001 HIS H 101 PHE 0.019 0.001 PHE F 456 TYR 0.021 0.001 TYR C 91 ARG 0.004 0.000 ARG F 454 Details of bonding type rmsd link_NAG-ASN : bond 0.00127 ( 2) link_NAG-ASN : angle 1.13165 ( 6) link_BETA1-4 : bond 0.01036 ( 1) link_BETA1-4 : angle 4.53436 ( 3) hydrogen bonds : bond 0.02959 ( 154) hydrogen bonds : angle 5.53920 ( 402) SS BOND : bond 0.00480 ( 7) SS BOND : angle 1.00726 ( 14) covalent geometry : bond 0.00271 ( 6922) covalent geometry : angle 0.69106 ( 9398) ********************** 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 227 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 190 time to evaluate : 0.821 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 34 MET cc_start: 0.7930 (mmm) cc_final: 0.7402 (mtt) REVERT: B 54 ASN cc_start: 0.8869 (t0) cc_final: 0.8409 (m-40) REVERT: B 89 GLU cc_start: 0.7650 (mp0) cc_final: 0.7343 (mp0) REVERT: D 10 GLU cc_start: 0.7085 (tm-30) cc_final: 0.6460 (tm-30) REVERT: D 23 LYS cc_start: 0.8198 (tttm) cc_final: 0.7833 (ttmm) REVERT: H 38 LYS cc_start: 0.8899 (OUTLIER) cc_final: 0.8579 (ttmm) REVERT: I 21 MET cc_start: 0.5694 (mmm) cc_final: 0.5405 (mmm) REVERT: I 97 TYR cc_start: 0.8537 (OUTLIER) cc_final: 0.8043 (p90) REVERT: L 38 LYS cc_start: 0.9235 (tppp) cc_final: 0.8750 (ttpt) REVERT: L 76 ARG cc_start: 0.8130 (tmm160) cc_final: 0.7904 (tmm160) REVERT: L 78 GLU cc_start: 0.8340 (tt0) cc_final: 0.7974 (tt0) outliers start: 37 outliers final: 32 residues processed: 208 average time/residue: 0.2272 time to fit residues: 60.0817 Evaluate side-chains 217 residues out of total 729 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 183 time to evaluate : 0.820 ------------------------------------------------------------------------------- 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 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 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 101 HIS 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 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 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 51 optimal weight: 0.9980 chunk 70 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 0.8980 chunk 38 optimal weight: 3.9990 chunk 47 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 79 optimal weight: 2.9990 chunk 27 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3842 r_free = 0.3842 target = 0.139267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3385 r_free = 0.3385 target = 0.106253 restraints weight = 12671.979| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3436 r_free = 0.3436 target = 0.109731 restraints weight = 8311.658| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.112082 restraints weight = 6351.419| |-----------------------------------------------------------------------------| r_work (final): 0.3484 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.4426 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 6932 Z= 0.183 Angle : 0.737 11.165 9421 Z= 0.368 Chirality : 0.045 0.198 1006 Planarity : 0.004 0.057 1199 Dihedral : 5.888 49.297 1015 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 11.29 Ramachandran Plot: Outliers : 0.12 % Allowed : 7.79 % Favored : 92.09 % Rotamer: Outliers : 5.35 % Allowed : 26.89 % 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: -1.79 (0.28), residues: 847 helix: -4.61 (0.92), residues: 14 sheet: -0.03 (0.28), residues: 339 loop : -2.02 (0.27), residues: 494 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 353 HIS 0.003 0.001 HIS B 35 PHE 0.020 0.002 PHE I 100 TYR 0.028 0.002 TYR C 91 ARG 0.004 0.001 ARG D 99 Details of bonding type rmsd link_NAG-ASN : bond 0.00034 ( 2) link_NAG-ASN : angle 1.34062 ( 6) link_BETA1-4 : bond 0.01222 ( 1) link_BETA1-4 : angle 4.30270 ( 3) hydrogen bonds : bond 0.03273 ( 154) hydrogen bonds : angle 5.69506 ( 402) SS BOND : bond 0.00510 ( 7) SS BOND : angle 1.22938 ( 14) covalent geometry : bond 0.00432 ( 6922) covalent geometry : angle 0.73192 ( 9398) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2904.03 seconds wall clock time: 50 minutes 58.52 seconds (3058.52 seconds total)