Starting phenix.real_space_refine on Wed Sep 17 03:06:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dme_47002/09_2025/9dme_47002_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dme_47002/09_2025/9dme_47002.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dme_47002/09_2025/9dme_47002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dme_47002/09_2025/9dme_47002.map" model { file = "/net/cci-nas-00/data/ceres_data/9dme_47002/09_2025/9dme_47002_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dme_47002/09_2025/9dme_47002_neut.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 1605 2.51 5 N 420 2.21 5 O 420 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2475 Number of models: 1 Model: "" Number of chains: 45 Chain: "J" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "J" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "L" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "F" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "G" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "I" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "M" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "O" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "N" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "E" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 156 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 156 Unusual residues: {'ACE': 1} Classifications: {'peptide': 21, 'undetermined': 1} Link IDs: {'ACE_C-N': 1, 'PTRANS': 2, 'TRANS': 18} Chain: "H" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {'NH2': 1} Classifications: {'undetermined': 1} Chain: "J" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "L" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "F" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "G" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "I" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "M" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "O" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "K" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "N" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Chain: "H" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 8 Unusual residues: {'8VH': 1} Classifications: {'undetermined': 1} Time building chain proxies: 0.91, per 1000 atoms: 0.37 Number of scatterers: 2475 At special positions: 0 Unit cell: (69.87, 69.87, 41.922, 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 420 8.00 N 420 7.00 C 1605 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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=52, symmetry=0 Number of additional bonds: simple=52, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.43 Conformation dependent library (CDL) restraints added in 115.6 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 540 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 19.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 298 through 299 Processing sheet with id=AA2, first strand: chain 'A' and resid 305 through 308 removed outlier: 6.684A pdb=" N SER J 305 " --> pdb=" O VAL G 306 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE G 308 " --> pdb=" O SER J 305 " (cutoff:3.500A) removed outlier: 6.378A pdb=" N GLN J 307 " --> pdb=" O ILE G 308 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 298 through 299 Processing sheet with id=AA4, first strand: chain 'C' and resid 305 through 308 removed outlier: 6.679A pdb=" N SER L 305 " --> pdb=" O VAL I 306 " (cutoff:3.500A) removed outlier: 8.133A pdb=" N ILE I 308 " --> pdb=" O SER L 305 " (cutoff:3.500A) removed outlier: 6.371A pdb=" N GLN L 307 " --> pdb=" O ILE I 308 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'N' and resid 298 through 299 Processing sheet with id=AA6, first strand: chain 'N' and resid 305 through 308 removed outlier: 6.684A pdb=" N SER K 305 " --> pdb=" O VAL N 306 " (cutoff:3.500A) removed outlier: 8.137A pdb=" N ILE N 308 " --> pdb=" O SER K 305 " (cutoff:3.500A) removed outlier: 6.375A pdb=" N GLN K 307 " --> pdb=" O ILE N 308 " (cutoff:3.500A) removed outlier: 6.696A pdb=" N SER E 305 " --> pdb=" O VAL H 306 " (cutoff:3.500A) removed outlier: 8.153A pdb=" N ILE H 308 " --> pdb=" O SER E 305 " (cutoff:3.500A) removed outlier: 6.390A pdb=" N GLN E 307 " --> pdb=" O ILE H 308 " (cutoff:3.500A) 36 hydrogen bonds defined for protein. 108 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.33 Time building geometry restraints manager: 0.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 390 1.30 - 1.43: 630 1.43 - 1.56: 1455 1.56 - 1.69: 0 1.69 - 1.82: 30 Bond restraints: 2505 Sorted by residual: bond pdb=" C ACE O 293 " pdb=" O ACE O 293 " ideal model delta sigma weight residual 1.199 1.238 -0.039 2.00e-02 2.50e+03 3.77e+00 bond pdb=" C ACE F 293 " pdb=" O ACE F 293 " ideal model delta sigma weight residual 1.199 1.238 -0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" C ACE A 293 " pdb=" O ACE A 293 " ideal model delta sigma weight residual 1.199 1.238 -0.039 2.00e-02 2.50e+03 3.74e+00 bond pdb=" C ACE M 293 " pdb=" O ACE M 293 " ideal model delta sigma weight residual 1.199 1.238 -0.039 2.00e-02 2.50e+03 3.71e+00 bond pdb=" C ACE I 293 " pdb=" O ACE I 293 " ideal model delta sigma weight residual 1.199 1.238 -0.039 2.00e-02 2.50e+03 3.71e+00 ... (remaining 2500 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.06: 3052 1.06 - 2.11: 211 2.11 - 3.16: 48 3.16 - 4.22: 34 4.22 - 5.27: 30 Bond angle restraints: 3375 Sorted by residual: angle pdb=" C TYR N 310 " pdb=" N LYS N 311 " pdb=" CA LYS N 311 " ideal model delta sigma weight residual 121.80 126.66 -4.86 2.44e+00 1.68e-01 3.96e+00 angle pdb=" C TYR E 310 " pdb=" N LYS E 311 " pdb=" CA LYS E 311 " ideal model delta sigma weight residual 121.80 126.65 -4.85 2.44e+00 1.68e-01 3.95e+00 angle pdb=" C TYR H 310 " pdb=" N LYS H 311 " pdb=" CA LYS H 311 " ideal model delta sigma weight residual 121.80 126.65 -4.85 2.44e+00 1.68e-01 3.95e+00 angle pdb=" C TYR K 310 " pdb=" N LYS K 311 " pdb=" CA LYS K 311 " ideal model delta sigma weight residual 121.80 126.63 -4.83 2.44e+00 1.68e-01 3.92e+00 angle pdb=" C TYR B 310 " pdb=" N LYS B 311 " pdb=" CA LYS B 311 " ideal model delta sigma weight residual 121.80 126.63 -4.83 2.44e+00 1.68e-01 3.92e+00 ... (remaining 3370 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.51: 1210 7.51 - 15.01: 124 15.01 - 22.51: 61 22.51 - 30.02: 25 30.02 - 37.52: 5 Dihedral angle restraints: 1425 sinusoidal: 570 harmonic: 855 Sorted by residual: dihedral pdb=" CH3 ACE N 293 " pdb=" C ACE N 293 " pdb=" N CYS N 294 " pdb=" CA CYS N 294 " ideal model delta sinusoidal sigma weight residual 180.00 165.74 14.26 1 5.00e+00 4.00e-02 1.18e+01 dihedral pdb=" CH3 ACE B 293 " pdb=" C ACE B 293 " pdb=" N CYS B 294 " pdb=" CA CYS B 294 " ideal model delta sinusoidal sigma weight residual 180.00 167.69 12.31 1 5.00e+00 4.00e-02 8.83e+00 dihedral pdb=" CH3 ACE H 293 " pdb=" C ACE H 293 " pdb=" N CYS H 294 " pdb=" CA CYS H 294 " ideal model delta sinusoidal sigma weight residual 180.00 167.69 12.31 1 5.00e+00 4.00e-02 8.83e+00 ... (remaining 1422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 128 0.026 - 0.052: 106 0.052 - 0.078: 20 0.078 - 0.104: 4 0.104 - 0.130: 102 Chirality restraints: 360 Sorted by residual: chirality pdb=" CA PRO G 301 " pdb=" N PRO G 301 " pdb=" C PRO G 301 " pdb=" CB PRO G 301 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA PRO F 301 " pdb=" N PRO F 301 " pdb=" C PRO F 301 " pdb=" CB PRO F 301 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.21e-01 chirality pdb=" CA PRO M 301 " pdb=" N PRO M 301 " pdb=" C PRO M 301 " pdb=" CB PRO M 301 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.17e-01 ... (remaining 357 not shown) Planarity restraints: 435 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ACE N 293 " 0.007 2.00e-02 2.50e+03 7.52e-02 7.07e+01 pdb=" O ACE N 293 " 0.020 2.00e-02 2.50e+03 pdb=" CH3 ACE N 293 " -0.064 2.00e-02 2.50e+03 pdb=" N CYS N 294 " 0.126 2.00e-02 2.50e+03 pdb=" CA CYS N 294 " -0.089 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE H 293 " 0.014 2.00e-02 2.50e+03 6.03e-02 4.55e+01 pdb=" O ACE H 293 " 0.010 2.00e-02 2.50e+03 pdb=" CH3 ACE H 293 " -0.053 2.00e-02 2.50e+03 pdb=" N CYS H 294 " 0.100 2.00e-02 2.50e+03 pdb=" CA CYS H 294 " -0.071 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ACE B 293 " 0.015 2.00e-02 2.50e+03 6.02e-02 4.53e+01 pdb=" O ACE B 293 " 0.010 2.00e-02 2.50e+03 pdb=" CH3 ACE B 293 " -0.053 2.00e-02 2.50e+03 pdb=" N CYS B 294 " 0.100 2.00e-02 2.50e+03 pdb=" CA CYS B 294 " -0.071 2.00e-02 2.50e+03 ... (remaining 432 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 566 2.80 - 3.32: 2159 3.32 - 3.85: 4260 3.85 - 4.37: 4626 4.37 - 4.90: 10021 Nonbonded interactions: 21632 Sorted by model distance: nonbonded pdb=" NZ LYS J 311 " pdb=" O CYS E 294 " model vdw 2.273 3.120 nonbonded pdb=" OH TYR D 310 " pdb=" OD2 ASP N 295 " model vdw 2.277 3.040 nonbonded pdb=" NZ LYS G 311 " pdb=" O CYS H 294 " model vdw 2.277 3.120 nonbonded pdb=" NZ LYS D 311 " pdb=" O CYS K 294 " model vdw 2.278 3.120 nonbonded pdb=" NZ LYS A 311 " pdb=" O CYS N 294 " model vdw 2.279 3.120 ... (remaining 21627 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.01 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' selection = chain 'M' selection = chain 'N' selection = chain 'O' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.370 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: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 5.220 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 9.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 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 : 0.035 0.726 2557 Z= 3.493 Angle : 0.822 5.274 3375 Z= 0.388 Chirality : 0.067 0.130 360 Planarity : 0.010 0.075 435 Dihedral : 8.679 37.521 885 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 17.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 11.11 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.67 (0.60), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.50 (0.45), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.002 0.001 TYR G 310 HIS 0.002 0.001 HIS O 299 Details of bonding type rmsd covalent geometry : bond 0.00550 ( 2505) covalent geometry : angle 0.82206 ( 3375) hydrogen bonds : bond 0.12912 ( 36) hydrogen bonds : angle 7.61507 ( 108) Misc. bond : bond 0.24439 ( 52) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 17 time to evaluate : 0.095 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.0533 time to fit residues: 1.2240 Evaluate side-chains 15 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 15 time to evaluate : 0.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 15 optimal weight: 6.9990 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.167080 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.146386 restraints weight = 2596.549| |-----------------------------------------------------------------------------| r_work (start): 0.4357 rms_B_bonded: 2.78 r_work: 0.4189 rms_B_bonded: 3.63 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2557 Z= 0.149 Angle : 0.770 5.482 3375 Z= 0.355 Chirality : 0.066 0.138 360 Planarity : 0.006 0.035 435 Dihedral : 6.207 54.547 345 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 5.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.32 % Favored : 93.68 % Rotamer: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.58), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.49 (0.45), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR G 310 HIS 0.002 0.001 HIS G 299 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 2505) covalent geometry : angle 0.76984 ( 3375) hydrogen bonds : bond 0.01848 ( 36) hydrogen bonds : angle 4.40611 ( 108) Misc. bond : bond 0.00090 ( 52) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 12 time to evaluate : 0.126 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0211 time to fit residues: 0.5647 Evaluate side-chains 11 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 11 time to evaluate : 0.144 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 23 optimal weight: 0.4980 chunk 6 optimal weight: 8.9990 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 7.9990 chunk 4 optimal weight: 5.9990 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 3.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4417 r_free = 0.4417 target = 0.154856 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4288 r_free = 0.4288 target = 0.137913 restraints weight = 2891.350| |-----------------------------------------------------------------------------| r_work (start): 0.4316 rms_B_bonded: 2.48 r_work: 0.4135 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.4135 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6804 moved from start: 0.2739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 2557 Z= 0.265 Angle : 0.953 6.458 3375 Z= 0.452 Chirality : 0.070 0.153 360 Planarity : 0.009 0.052 435 Dihedral : 6.779 59.843 345 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.82 % Favored : 90.18 % Rotamer: Outliers : 2.22 % Allowed : 8.89 % Favored : 88.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.48 (0.55), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.11 (0.42), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR N 310 HIS 0.003 0.001 HIS N 299 Details of bonding type rmsd covalent geometry : bond 0.00710 ( 2505) covalent geometry : angle 0.95340 ( 3375) hydrogen bonds : bond 0.02155 ( 36) hydrogen bonds : angle 4.09982 ( 108) Misc. bond : bond 0.00126 ( 52) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 17 time to evaluate : 0.098 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 20 average time/residue: 0.0548 time to fit residues: 1.4382 Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain K residue 300 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 4.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 26 optimal weight: 0.0170 chunk 8 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5620 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.170339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4422 r_free = 0.4422 target = 0.151271 restraints weight = 2582.936| |-----------------------------------------------------------------------------| r_work (start): 0.4436 rms_B_bonded: 2.50 r_work: 0.4281 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6593 moved from start: 0.2677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2557 Z= 0.119 Angle : 0.717 5.683 3375 Z= 0.335 Chirality : 0.066 0.135 360 Planarity : 0.006 0.039 435 Dihedral : 6.356 54.105 345 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.59 % Allowed : 7.04 % Favored : 90.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.95 (0.57), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.71 (0.44), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.000 TYR J 310 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 2505) covalent geometry : angle 0.71711 ( 3375) hydrogen bonds : bond 0.01259 ( 36) hydrogen bonds : angle 3.80365 ( 108) Misc. bond : bond 0.00075 ( 52) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 12 time to evaluate : 0.075 Fit side-chains outliers start: 7 outliers final: 1 residues processed: 18 average time/residue: 0.0206 time to fit residues: 0.7135 Evaluate side-chains 13 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 12 time to evaluate : 0.095 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 8 optimal weight: 3.9990 chunk 19 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 4.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 0.9980 chunk 7 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 15 optimal weight: 3.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4513 r_free = 0.4513 target = 0.162225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.141563 restraints weight = 2794.330| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.72 r_work: 0.4166 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.4166 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6731 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 2557 Z= 0.172 Angle : 0.824 6.250 3375 Z= 0.389 Chirality : 0.068 0.137 360 Planarity : 0.007 0.043 435 Dihedral : 6.159 56.262 345 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer: Outliers : 0.74 % Allowed : 7.04 % Favored : 92.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.91 (0.57), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.68 (0.43), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR N 310 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00449 ( 2505) covalent geometry : angle 0.82435 ( 3375) hydrogen bonds : bond 0.01322 ( 36) hydrogen bonds : angle 3.99911 ( 108) Misc. bond : bond 0.00084 ( 52) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.095 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 14 average time/residue: 0.0361 time to fit residues: 0.8093 Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 0.8980 chunk 17 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 7 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 19 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4569 r_free = 0.4569 target = 0.168698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.145589 restraints weight = 3263.821| |-----------------------------------------------------------------------------| r_work (start): 0.4400 rms_B_bonded: 3.09 r_work: 0.4195 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.4195 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2557 Z= 0.137 Angle : 0.755 5.899 3375 Z= 0.354 Chirality : 0.067 0.135 360 Planarity : 0.006 0.039 435 Dihedral : 5.950 54.008 345 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.11 % Allowed : 7.04 % Favored : 91.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.97 (0.56), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.73 (0.43), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.005 0.001 TYR H 310 HIS 0.003 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00348 ( 2505) covalent geometry : angle 0.75539 ( 3375) hydrogen bonds : bond 0.01105 ( 36) hydrogen bonds : angle 3.45228 ( 108) Misc. bond : bond 0.00077 ( 52) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.058 Fit side-chains REVERT: N 311 LYS cc_start: 0.6171 (mttt) cc_final: 0.5884 (mtpt) outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 0.0234 time to fit residues: 0.5987 Evaluate side-chains 17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 20 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 10.0000 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.159806 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4332 r_free = 0.4332 target = 0.138881 restraints weight = 3109.392| |-----------------------------------------------------------------------------| r_work (start): 0.4349 rms_B_bonded: 2.85 r_work: 0.4141 rms_B_bonded: 3.64 restraints_weight: 0.5000 r_work (final): 0.4141 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6759 moved from start: 0.3123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 2557 Z= 0.183 Angle : 0.843 6.434 3375 Z= 0.396 Chirality : 0.068 0.143 360 Planarity : 0.007 0.045 435 Dihedral : 5.850 54.360 345 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 1.11 % Allowed : 8.15 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.19 (0.55), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.42), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.007 0.001 TYR G 310 HIS 0.005 0.001 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00486 ( 2505) covalent geometry : angle 0.84277 ( 3375) hydrogen bonds : bond 0.01179 ( 36) hydrogen bonds : angle 3.29736 ( 108) Misc. bond : bond 0.00087 ( 52) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 16 time to evaluate : 0.085 Fit side-chains REVERT: N 311 LYS cc_start: 0.6338 (mttt) cc_final: 0.6032 (mtpt) outliers start: 3 outliers final: 2 residues processed: 17 average time/residue: 0.0331 time to fit residues: 0.8278 Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 300 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 24 optimal weight: 5.9990 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 4.9990 chunk 16 optimal weight: 0.4980 chunk 22 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 20 optimal weight: 0.1980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.169661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.146396 restraints weight = 3241.542| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 3.07 r_work: 0.4211 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.4211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.3151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2557 Z= 0.124 Angle : 0.745 5.700 3375 Z= 0.347 Chirality : 0.066 0.132 360 Planarity : 0.006 0.041 435 Dihedral : 5.073 40.240 345 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.11 % Allowed : 7.78 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.09 (0.55), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.82 (0.42), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.004 0.001 TYR N 310 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 2505) covalent geometry : angle 0.74525 ( 3375) hydrogen bonds : bond 0.00995 ( 36) hydrogen bonds : angle 3.17764 ( 108) Misc. bond : bond 0.00065 ( 52) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 15 time to evaluate : 0.151 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 16 average time/residue: 0.0308 time to fit residues: 0.7648 Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 14 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 300 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 0.5980 chunk 21 optimal weight: 6.9990 chunk 4 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 10.0000 chunk 17 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 22 optimal weight: 5.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.158766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4325 r_free = 0.4325 target = 0.137742 restraints weight = 3129.377| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.84 r_work: 0.4129 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.4129 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6791 moved from start: 0.3324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.049 2557 Z= 0.215 Angle : 0.900 6.756 3375 Z= 0.424 Chirality : 0.070 0.148 360 Planarity : 0.008 0.047 435 Dihedral : 5.246 37.677 345 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 12.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.42 % Favored : 91.58 % Rotamer: Outliers : 0.74 % Allowed : 7.78 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.42 (0.54), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.07 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.011 0.002 TYR N 310 HIS 0.006 0.002 HIS I 299 Details of bonding type rmsd covalent geometry : bond 0.00568 ( 2505) covalent geometry : angle 0.89971 ( 3375) hydrogen bonds : bond 0.01183 ( 36) hydrogen bonds : angle 3.35494 ( 108) Misc. bond : bond 0.00101 ( 52) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.116 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0480 time to fit residues: 1.1433 Evaluate side-chains 17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 10.0000 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.6980 chunk 27 optimal weight: 7.9990 chunk 14 optimal weight: 0.9980 chunk 11 optimal weight: 3.9990 chunk 18 optimal weight: 0.0470 overall best weight: 0.6478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 299 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4613 r_free = 0.4613 target = 0.170264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.147331 restraints weight = 3026.466| |-----------------------------------------------------------------------------| r_work (start): 0.4416 rms_B_bonded: 2.94 r_work: 0.4242 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4242 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6650 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2557 Z= 0.123 Angle : 0.751 5.827 3375 Z= 0.349 Chirality : 0.066 0.129 360 Planarity : 0.007 0.041 435 Dihedral : 5.112 39.529 345 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Rotamer: Outliers : 0.74 % Allowed : 8.52 % Favored : 90.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.23 (0.54), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.93 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR J 310 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00301 ( 2505) covalent geometry : angle 0.75100 ( 3375) hydrogen bonds : bond 0.00989 ( 36) hydrogen bonds : angle 3.20759 ( 108) Misc. bond : bond 0.00064 ( 52) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 570 Ramachandran restraints generated. 285 Oldfield, 0 Emsley, 285 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 19 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 17 time to evaluate : 0.096 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 17 average time/residue: 0.0335 time to fit residues: 0.8695 Evaluate side-chains 18 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 16 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 300 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 4.9990 chunk 5 optimal weight: 0.9980 chunk 7 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 4.9990 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 23 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4607 r_free = 0.4607 target = 0.169870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4406 r_free = 0.4406 target = 0.146026 restraints weight = 3312.667| |-----------------------------------------------------------------------------| r_work (start): 0.4403 rms_B_bonded: 3.12 r_work: 0.4219 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6673 moved from start: 0.3394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2557 Z= 0.128 Angle : 0.759 6.066 3375 Z= 0.350 Chirality : 0.066 0.133 360 Planarity : 0.006 0.040 435 Dihedral : 5.076 39.967 345 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.61 % Favored : 94.39 % Rotamer: Outliers : 0.74 % Allowed : 8.15 % Favored : 91.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.16 (0.55), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.42), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TYR 0.006 0.001 TYR N 310 HIS 0.004 0.001 HIS A 299 Details of bonding type rmsd covalent geometry : bond 0.00317 ( 2505) covalent geometry : angle 0.75916 ( 3375) hydrogen bonds : bond 0.00936 ( 36) hydrogen bonds : angle 3.14128 ( 108) Misc. bond : bond 0.00067 ( 52) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 736.81 seconds wall clock time: 13 minutes 27.69 seconds (807.69 seconds total)