Starting phenix.real_space_refine on Wed Jun 4 11:33:23 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dme_47002/06_2025/9dme_47002_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dme_47002/06_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_47002/06_2025/9dme_47002.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dme_47002/06_2025/9dme_47002.map" model { file = "/net/cci-nas-00/data/ceres_data/9dme_47002/06_2025/9dme_47002_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dme_47002/06_2025/9dme_47002_neut.cif" } resolution = 3.2 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= 0.002 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-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 2.54, per 1000 atoms: 1.03 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: 0.91 Conformation dependent library (CDL) restraints added in 286.9 milliseconds 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: 0.34 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: 0.57 Time building geometry restraints manager: 0.95 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: 0.00 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: 1.960 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.450 Find NCS groups from input model: 0.170 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: 0.010 Load rotamer database and sin/cos tables:3.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.000 ------------------------------------------------------------------------------- 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 (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: -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 HIS 0.002 0.001 HIS O 299 TYR 0.002 0.001 TYR G 310 Details of bonding type rmsd hydrogen bonds : bond 0.12912 ( 36) hydrogen bonds : angle 7.61507 ( 108) covalent geometry : bond 0.00550 ( 2505) covalent geometry : angle 0.82206 ( 3375) 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 : 0.273 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 17 average time/residue: 0.1099 time to fit residues: 2.6255 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 : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 7.9990 chunk 22 optimal weight: 0.4980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.4481 r_free = 0.4481 target = 0.165063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.145149 restraints weight = 2567.998| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.63 r_work: 0.4184 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.4184 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2557 Z= 0.168 Angle : 0.810 5.489 3375 Z= 0.374 Chirality : 0.067 0.143 360 Planarity : 0.007 0.038 435 Dihedral : 6.157 56.157 345 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % 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 (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: -0.74 (0.58), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.44), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS J 299 TYR 0.006 0.001 TYR G 310 Details of bonding type rmsd hydrogen bonds : bond 0.01860 ( 36) hydrogen bonds : angle 4.50857 ( 108) covalent geometry : bond 0.00431 ( 2505) covalent geometry : angle 0.80955 ( 3375) Misc. bond : bond 0.00112 ( 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 13 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 13 time to evaluate : 0.282 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 0.0505 time to fit residues: 1.3599 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 : 0.266 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 3.9990 chunk 15 optimal weight: 7.9990 chunk 28 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 0 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 overall best weight: 2.1186 ------------------------------------------------------------------------------- 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 = 0.4421 r_free = 0.4421 target = 0.156229 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4290 r_free = 0.4290 target = 0.138595 restraints weight = 2781.992| |-----------------------------------------------------------------------------| r_work (start): 0.4310 rms_B_bonded: 2.52 r_work: 0.4133 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work (final): 0.4133 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6767 moved from start: 0.2563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.052 2557 Z= 0.236 Angle : 0.901 6.076 3375 Z= 0.426 Chirality : 0.068 0.149 360 Planarity : 0.008 0.047 435 Dihedral : 6.512 56.893 345 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 10.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % 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 (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: -1.30 (0.55), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.98 (0.42), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS A 299 TYR 0.009 0.001 TYR N 310 Details of bonding type rmsd hydrogen bonds : bond 0.02011 ( 36) hydrogen bonds : angle 4.04799 ( 108) covalent geometry : bond 0.00625 ( 2505) covalent geometry : angle 0.90130 ( 3375) Misc. bond : bond 0.00139 ( 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 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 16 time to evaluate : 0.313 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 20 average time/residue: 0.1017 time to fit residues: 2.9496 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 : 0.282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 chunk 21 optimal weight: 7.9990 chunk 4 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 18 optimal weight: 2.9990 chunk 12 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 15 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.4412 r_free = 0.4412 target = 0.153814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.135113 restraints weight = 3464.997| |-----------------------------------------------------------------------------| r_work (start): 0.4270 rms_B_bonded: 2.83 r_work: 0.4073 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.4073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6922 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.077 2557 Z= 0.343 Angle : 1.045 7.071 3375 Z= 0.504 Chirality : 0.073 0.169 360 Planarity : 0.010 0.059 435 Dihedral : 6.632 55.942 345 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 16.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.47 % Favored : 90.53 % Rotamer: Outliers : 2.59 % Allowed : 7.41 % Favored : 90.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -2.30 (0.50), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.75 (0.38), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS D 299 TYR 0.013 0.002 TYR N 310 Details of bonding type rmsd hydrogen bonds : bond 0.01948 ( 36) hydrogen bonds : angle 4.02492 ( 108) covalent geometry : bond 0.00914 ( 2505) covalent geometry : angle 1.04482 ( 3375) Misc. bond : bond 0.00148 ( 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 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 18 time to evaluate : 0.274 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 21 average time/residue: 0.1647 time to fit residues: 4.3278 Evaluate side-chains 22 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 18 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain C residue 300 VAL Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain K residue 300 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 26 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 6.9990 chunk 7 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 299 HIS O 299 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4559 r_free = 0.4559 target = 0.166915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.144538 restraints weight = 2853.422| |-----------------------------------------------------------------------------| r_work (start): 0.4397 rms_B_bonded: 2.81 r_work: 0.4191 rms_B_bonded: 3.79 restraints_weight: 0.5000 r_work (final): 0.4191 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6715 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2557 Z= 0.137 Angle : 0.776 5.811 3375 Z= 0.368 Chirality : 0.068 0.139 360 Planarity : 0.007 0.045 435 Dihedral : 5.726 46.791 345 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.48 % Allowed : 8.89 % Favored : 89.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.52 (0.53), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.15 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 299 TYR 0.007 0.001 TYR G 310 Details of bonding type rmsd hydrogen bonds : bond 0.01236 ( 36) hydrogen bonds : angle 3.52900 ( 108) covalent geometry : bond 0.00348 ( 2505) covalent geometry : angle 0.77643 ( 3375) Misc. bond : bond 0.00073 ( 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 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.248 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 18 average time/residue: 0.1067 time to fit residues: 2.7061 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 : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 12 optimal weight: 5.9990 chunk 2 optimal weight: 10.0000 chunk 15 optimal weight: 0.9990 chunk 7 optimal weight: 3.9990 chunk 27 optimal weight: 4.9990 chunk 25 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- 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 = 0.4522 r_free = 0.4522 target = 0.162562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4341 r_free = 0.4341 target = 0.140154 restraints weight = 3054.155| |-----------------------------------------------------------------------------| r_work (start): 0.4363 rms_B_bonded: 2.88 r_work: 0.4147 rms_B_bonded: 3.77 restraints_weight: 0.5000 r_work (final): 0.4147 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6761 moved from start: 0.3216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 2557 Z= 0.157 Angle : 0.811 6.194 3375 Z= 0.381 Chirality : 0.068 0.137 360 Planarity : 0.007 0.045 435 Dihedral : 5.359 37.007 345 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 10.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.74 % Allowed : 10.00 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.39 (0.54), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.05 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS I 299 TYR 0.005 0.001 TYR N 310 Details of bonding type rmsd hydrogen bonds : bond 0.01208 ( 36) hydrogen bonds : angle 3.39061 ( 108) covalent geometry : bond 0.00410 ( 2505) covalent geometry : angle 0.81061 ( 3375) Misc. bond : bond 0.00082 ( 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 17 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 15 time to evaluate : 0.301 Fit side-chains REVERT: D 311 LYS cc_start: 0.6363 (mttt) cc_final: 0.6016 (mtpt) REVERT: N 311 LYS cc_start: 0.6330 (mttt) cc_final: 0.6095 (mtpt) outliers start: 2 outliers final: 2 residues processed: 15 average time/residue: 0.1498 time to fit residues: 3.0197 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 : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL Chi-restraints excluded: chain C residue 300 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 14 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 17 optimal weight: 0.9990 chunk 26 optimal weight: 0.0040 chunk 24 optimal weight: 0.5980 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4600 r_free = 0.4600 target = 0.170707 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4409 r_free = 0.4409 target = 0.146609 restraints weight = 3095.900| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 3.04 r_work: 0.4222 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6641 moved from start: 0.3273 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= 0.116 Angle : 0.728 5.699 3375 Z= 0.338 Chirality : 0.066 0.131 360 Planarity : 0.006 0.040 435 Dihedral : 5.337 39.047 345 Min Nonbonded Distance : 2.411 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.22 % Allowed : 9.63 % Favored : 88.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.21 (0.55), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.91 (0.42), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS K 299 TYR 0.003 0.001 TYR G 310 Details of bonding type rmsd hydrogen bonds : bond 0.01038 ( 36) hydrogen bonds : angle 3.23807 ( 108) covalent geometry : bond 0.00289 ( 2505) covalent geometry : angle 0.72764 ( 3375) Misc. bond : bond 0.00065 ( 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 25 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 19 time to evaluate : 0.288 Fit side-chains REVERT: D 311 LYS cc_start: 0.6140 (mttt) cc_final: 0.5827 (mtpt) REVERT: N 311 LYS cc_start: 0.6179 (mttt) cc_final: 0.5917 (mtpt) outliers start: 6 outliers final: 3 residues processed: 22 average time/residue: 0.1416 time to fit residues: 4.0489 Evaluate side-chains 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 17 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL 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 6 optimal weight: 8.9990 chunk 22 optimal weight: 6.9990 chunk 21 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 17 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 299 HIS C 299 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4475 r_free = 0.4475 target = 0.157997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.135930 restraints weight = 3373.093| |-----------------------------------------------------------------------------| r_work (start): 0.4306 rms_B_bonded: 2.96 r_work: 0.4108 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.4108 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6818 moved from start: 0.3477 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= 0.218 Angle : 0.911 6.994 3375 Z= 0.428 Chirality : 0.070 0.150 360 Planarity : 0.008 0.049 435 Dihedral : 5.505 35.835 345 Min Nonbonded Distance : 2.385 Molprobity Statistics. All-atom Clashscore : 13.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.12 % Favored : 90.88 % Rotamer: Outliers : 1.11 % Allowed : 9.63 % Favored : 89.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % 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: -1.56 (0.54), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.18 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS I 299 TYR 0.011 0.002 TYR N 310 Details of bonding type rmsd hydrogen bonds : bond 0.01250 ( 36) hydrogen bonds : angle 3.39935 ( 108) covalent geometry : bond 0.00578 ( 2505) covalent geometry : angle 0.91105 ( 3375) Misc. bond : bond 0.00109 ( 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 : 0.307 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 15 average time/residue: 0.1182 time to fit residues: 2.5843 Evaluate side-chains 16 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 13 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 300 VAL 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 26 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 4 optimal weight: 6.9990 chunk 22 optimal weight: 0.5980 chunk 2 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 10 optimal weight: 0.7980 overall best weight: 0.8784 ------------------------------------------------------------------------------- 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 = 0.4553 r_free = 0.4553 target = 0.165089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4368 r_free = 0.4368 target = 0.142506 restraints weight = 2956.505| |-----------------------------------------------------------------------------| r_work (start): 0.4372 rms_B_bonded: 2.87 r_work: 0.4189 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.4189 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6721 moved from start: 0.3495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2557 Z= 0.138 Angle : 0.790 6.779 3375 Z= 0.368 Chirality : 0.067 0.132 360 Planarity : 0.007 0.045 435 Dihedral : 5.383 37.111 345 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 1.48 % Allowed : 10.00 % 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 (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: -1.45 (0.54), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.10 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS K 299 TYR 0.006 0.001 TYR G 310 Details of bonding type rmsd hydrogen bonds : bond 0.01066 ( 36) hydrogen bonds : angle 3.30325 ( 108) covalent geometry : bond 0.00348 ( 2505) covalent geometry : angle 0.78952 ( 3375) Misc. bond : bond 0.00077 ( 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 20 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 16 time to evaluate : 0.299 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 17 average time/residue: 0.0752 time to fit residues: 2.1095 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 : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 26 optimal weight: 4.9990 chunk 1 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 5 optimal weight: 3.9990 chunk 18 optimal weight: 0.2980 chunk 27 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 7.9990 chunk 13 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 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 = 0.4577 r_free = 0.4577 target = 0.168333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4388 r_free = 0.4388 target = 0.142156 restraints weight = 3043.736| |-----------------------------------------------------------------------------| r_work (start): 0.4383 rms_B_bonded: 3.13 r_work: 0.4172 rms_B_bonded: 3.87 restraints_weight: 0.5000 r_work (final): 0.4172 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6665 moved from start: 0.3682 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= 0.220 Angle : 0.927 7.211 3375 Z= 0.436 Chirality : 0.069 0.149 360 Planarity : 0.008 0.051 435 Dihedral : 5.529 36.334 345 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 13.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.07 % Favored : 91.93 % Rotamer: Outliers : 0.74 % Allowed : 10.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.53), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.40), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS C 299 TYR 0.011 0.002 TYR N 310 Details of bonding type rmsd hydrogen bonds : bond 0.01286 ( 36) hydrogen bonds : angle 3.50622 ( 108) covalent geometry : bond 0.00578 ( 2505) covalent geometry : angle 0.92677 ( 3375) Misc. bond : bond 0.00109 ( 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 15 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.262 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 13 average time/residue: 0.0402 time to fit residues: 1.1379 Evaluate side-chains 15 residues out of total 270 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 13 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A 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 10 optimal weight: 0.7980 chunk 26 optimal weight: 0.0770 chunk 5 optimal weight: 0.8980 chunk 22 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7138 ------------------------------------------------------------------------------- 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 = 0.4584 r_free = 0.4584 target = 0.167725 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.144800 restraints weight = 2843.677| |-----------------------------------------------------------------------------| r_work (start): 0.4427 rms_B_bonded: 2.83 r_work: 0.4224 rms_B_bonded: 3.71 restraints_weight: 0.5000 r_work (final): 0.4224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6645 moved from start: 0.3665 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= 0.129 Angle : 0.770 6.091 3375 Z= 0.359 Chirality : 0.066 0.130 360 Planarity : 0.007 0.043 435 Dihedral : 5.368 37.479 345 Min Nonbonded Distance : 2.423 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 0.74 % Allowed : 10.37 % 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 (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: -1.59 (0.53), residues: 285 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.20 (0.41), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS N 299 TYR 0.006 0.001 TYR N 310 Details of bonding type rmsd hydrogen bonds : bond 0.01017 ( 36) hydrogen bonds : angle 3.30033 ( 108) covalent geometry : bond 0.00319 ( 2505) covalent geometry : angle 0.77006 ( 3375) Misc. bond : bond 0.00070 ( 52) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1528.30 seconds wall clock time: 27 minutes 17.92 seconds (1637.92 seconds total)