Starting phenix.real_space_refine on Fri Aug 22 14:00:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qx9_18715/08_2025/8qx9_18715.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qx9_18715/08_2025/8qx9_18715.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8qx9_18715/08_2025/8qx9_18715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qx9_18715/08_2025/8qx9_18715.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8qx9_18715/08_2025/8qx9_18715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qx9_18715/08_2025/8qx9_18715.map" } resolution = 3.76 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= 0.003 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 84 5.16 5 C 2232 2.51 5 N 660 2.21 5 O 720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3696 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Restraints were copied for chains: B, C, D, E, F, G, H, I, J, K, L Time building chain proxies: 0.49, per 1000 atoms: 0.13 Number of scatterers: 3696 At special positions: 0 Unit cell: (102.96, 84.24, 46.8, 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 84 16.00 O 720 8.00 N 660 7.00 C 2232 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=0, symmetry=0 Time building additional restraints: 0.21 Conformation dependent library (CDL) restraints added in 102.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 20.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA2, first strand: chain 'A' and resid 321 through 323 Processing sheet with id=AA3, first strand: chain 'A' and resid 328 through 334 removed outlier: 6.592A pdb=" N ALA A 329 " --> pdb=" O LEU C 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER C 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN A 331 " --> pdb=" O SER C 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP C 334 " --> pdb=" O GLN A 331 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER A 333 " --> pdb=" O TRP C 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA C 329 " --> pdb=" O LEU E 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER E 332 " --> pdb=" O ALA C 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN C 331 " --> pdb=" O SER E 332 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TRP E 334 " --> pdb=" O GLN C 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER C 333 " --> pdb=" O TRP E 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA E 329 " --> pdb=" O LEU G 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER G 332 " --> pdb=" O ALA E 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN E 331 " --> pdb=" O SER G 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP G 334 " --> pdb=" O GLN E 331 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER E 333 " --> pdb=" O TRP G 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA G 329 " --> pdb=" O LEU I 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER I 332 " --> pdb=" O ALA G 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN G 331 " --> pdb=" O SER I 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP I 334 " --> pdb=" O GLN G 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER G 333 " --> pdb=" O TRP I 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA I 329 " --> pdb=" O LEU K 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER K 332 " --> pdb=" O ALA I 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN I 331 " --> pdb=" O SER K 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP K 334 " --> pdb=" O GLN I 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER I 333 " --> pdb=" O TRP K 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 311 through 312 Processing sheet with id=AA5, first strand: chain 'B' and resid 321 through 323 Processing sheet with id=AA6, first strand: chain 'B' and resid 328 through 334 removed outlier: 6.592A pdb=" N ALA B 329 " --> pdb=" O LEU D 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER D 332 " --> pdb=" O ALA B 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN B 331 " --> pdb=" O SER D 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP D 334 " --> pdb=" O GLN B 331 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER B 333 " --> pdb=" O TRP D 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA D 329 " --> pdb=" O LEU F 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER F 332 " --> pdb=" O ALA D 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN D 331 " --> pdb=" O SER F 332 " (cutoff:3.500A) removed outlier: 8.203A pdb=" N TRP F 334 " --> pdb=" O GLN D 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER D 333 " --> pdb=" O TRP F 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA F 329 " --> pdb=" O LEU H 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER H 332 " --> pdb=" O ALA F 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN F 331 " --> pdb=" O SER H 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP H 334 " --> pdb=" O GLN F 331 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N SER F 333 " --> pdb=" O TRP H 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA H 329 " --> pdb=" O LEU J 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER J 332 " --> pdb=" O ALA H 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN H 331 " --> pdb=" O SER J 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP J 334 " --> pdb=" O GLN H 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER H 333 " --> pdb=" O TRP J 334 " (cutoff:3.500A) removed outlier: 6.592A pdb=" N ALA J 329 " --> pdb=" O LEU L 330 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N SER L 332 " --> pdb=" O ALA J 329 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N GLN J 331 " --> pdb=" O SER L 332 " (cutoff:3.500A) removed outlier: 8.204A pdb=" N TRP L 334 " --> pdb=" O GLN J 331 " (cutoff:3.500A) removed outlier: 6.761A pdb=" N SER J 333 " --> pdb=" O TRP L 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 30 hydrogen bonds defined for protein. 90 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: 0.44 Time building geometry restraints manager: 0.31 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 648 1.31 - 1.44: 972 1.44 - 1.56: 1956 1.56 - 1.69: 0 1.69 - 1.81: 168 Bond restraints: 3744 Sorted by residual: bond pdb=" C PRO E 320 " pdb=" O PRO E 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.42e+01 bond pdb=" C PRO F 320 " pdb=" O PRO F 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.42e+01 bond pdb=" C PRO D 320 " pdb=" O PRO D 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.42e+01 bond pdb=" C PRO C 320 " pdb=" O PRO C 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.42e+01 bond pdb=" C PRO J 320 " pdb=" O PRO J 320 " ideal model delta sigma weight residual 1.233 1.189 0.044 1.16e-02 7.43e+03 1.41e+01 ... (remaining 3739 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 2984 1.54 - 3.09: 1048 3.09 - 4.63: 716 4.63 - 6.18: 187 6.18 - 7.72: 45 Bond angle restraints: 4980 Sorted by residual: angle pdb=" N GLN E 327 " pdb=" CA GLN E 327 " pdb=" C GLN E 327 " ideal model delta sigma weight residual 111.36 105.16 6.20 1.09e+00 8.42e-01 3.24e+01 angle pdb=" N GLN I 327 " pdb=" CA GLN I 327 " pdb=" C GLN I 327 " ideal model delta sigma weight residual 111.36 105.16 6.20 1.09e+00 8.42e-01 3.23e+01 angle pdb=" N GLN J 327 " pdb=" CA GLN J 327 " pdb=" C GLN J 327 " ideal model delta sigma weight residual 111.36 105.16 6.20 1.09e+00 8.42e-01 3.23e+01 angle pdb=" N GLN K 327 " pdb=" CA GLN K 327 " pdb=" C GLN K 327 " ideal model delta sigma weight residual 111.36 105.17 6.19 1.09e+00 8.42e-01 3.23e+01 angle pdb=" N GLN L 327 " pdb=" CA GLN L 327 " pdb=" C GLN L 327 " ideal model delta sigma weight residual 111.36 105.17 6.19 1.09e+00 8.42e-01 3.23e+01 ... (remaining 4975 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.26: 1858 16.26 - 32.51: 218 32.51 - 48.76: 84 48.76 - 65.02: 12 65.02 - 81.27: 24 Dihedral angle restraints: 2196 sinusoidal: 780 harmonic: 1416 Sorted by residual: dihedral pdb=" C PHE K 316 " pdb=" N PHE K 316 " pdb=" CA PHE K 316 " pdb=" CB PHE K 316 " ideal model delta harmonic sigma weight residual -122.60 -114.64 -7.96 0 2.50e+00 1.60e-01 1.01e+01 dihedral pdb=" C PHE L 316 " pdb=" N PHE L 316 " pdb=" CA PHE L 316 " pdb=" CB PHE L 316 " ideal model delta harmonic sigma weight residual -122.60 -114.64 -7.96 0 2.50e+00 1.60e-01 1.01e+01 dihedral pdb=" C PHE G 316 " pdb=" N PHE G 316 " pdb=" CA PHE G 316 " pdb=" CB PHE G 316 " ideal model delta harmonic sigma weight residual -122.60 -114.65 -7.95 0 2.50e+00 1.60e-01 1.01e+01 ... (remaining 2193 not shown) Histogram of chiral volume deviations from ideal: 0.004 - 0.056: 182 0.056 - 0.107: 142 0.107 - 0.159: 84 0.159 - 0.210: 58 0.210 - 0.262: 14 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA TRP A 334 " pdb=" N TRP A 334 " pdb=" C TRP A 334 " pdb=" CB TRP A 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA TRP B 334 " pdb=" N TRP B 334 " pdb=" C TRP B 334 " pdb=" CB TRP B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.72e+00 chirality pdb=" CA TRP G 334 " pdb=" N TRP G 334 " pdb=" C TRP G 334 " pdb=" CB TRP G 334 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.70e+00 ... (remaining 477 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 334 " 0.028 2.00e-02 2.50e+03 1.75e-02 7.63e+00 pdb=" CG TRP C 334 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP C 334 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 334 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP C 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP C 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP C 334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 334 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 334 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP D 334 " 0.028 2.00e-02 2.50e+03 1.75e-02 7.63e+00 pdb=" CG TRP D 334 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP D 334 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP D 334 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP D 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP D 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP D 334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP D 334 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP D 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP D 334 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP L 334 " 0.028 2.00e-02 2.50e+03 1.75e-02 7.63e+00 pdb=" CG TRP L 334 " -0.046 2.00e-02 2.50e+03 pdb=" CD1 TRP L 334 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP L 334 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TRP L 334 " 0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP L 334 " -0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 334 " 0.006 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 334 " 0.001 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.50 - 2.98: 1576 2.98 - 3.46: 3594 3.46 - 3.94: 6298 3.94 - 4.42: 6843 4.42 - 4.90: 13577 Nonbonded interactions: 31888 Sorted by model distance: nonbonded pdb=" N ILE A 318 " pdb=" O ILE A 318 " model vdw 2.496 2.496 nonbonded pdb=" N ILE B 318 " pdb=" O ILE B 318 " model vdw 2.496 2.496 nonbonded pdb=" N ILE J 318 " pdb=" O ILE J 318 " model vdw 2.496 2.496 nonbonded pdb=" N ILE I 318 " pdb=" O ILE I 318 " model vdw 2.496 2.496 nonbonded pdb=" N ILE H 318 " pdb=" O ILE H 318 " model vdw 2.496 2.496 ... (remaining 31883 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.840 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: 0.020 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 4.690 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.000 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:1.220 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6797 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 : 0.014 0.044 3744 Z= 1.031 Angle : 2.173 7.720 4980 Z= 1.625 Chirality : 0.110 0.262 480 Planarity : 0.010 0.025 684 Dihedral : 18.791 81.271 1308 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 27.59 % Favored : 72.41 % 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: -4.75 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.61 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.003 PHE L 316 TRP 0.046 0.010 TRP C 334 Details of bonding type rmsd covalent geometry : bond 0.01385 ( 3744) covalent geometry : angle 2.17342 ( 4980) hydrogen bonds : bond 0.22508 ( 30) hydrogen bonds : angle 7.60692 ( 90) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 172 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 172 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 336 MET cc_start: 0.7377 (ttt) cc_final: 0.7018 (ttt) REVERT: B 336 MET cc_start: 0.7398 (ttt) cc_final: 0.7028 (ttt) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.0513 time to fit residues: 11.4601 Evaluate side-chains 160 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 GLN B 331 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 346 GLN ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN ** G 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 331 GLN ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 327 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 327 GLN L 327 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5247 r_free = 0.5247 target = 0.393530 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.5684 r_free = 0.5684 target = 0.291411 restraints weight = 5029.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.5720 r_free = 0.5720 target = 0.294164 restraints weight = 3760.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.5724 r_free = 0.5724 target = 0.295493 restraints weight = 3122.620| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.5726 r_free = 0.5726 target = 0.295907 restraints weight = 2795.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5729 r_free = 0.5729 target = 0.297108 restraints weight = 2674.375| |-----------------------------------------------------------------------------| r_work (final): 0.5115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7034 moved from start: 0.4075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 3744 Z= 0.135 Angle : 0.625 5.019 4980 Z= 0.332 Chirality : 0.040 0.113 480 Planarity : 0.003 0.016 684 Dihedral : 5.553 16.774 528 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 2.01 % Allowed : 27.30 % Favored : 70.69 % 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: -4.60 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.009 0.003 PHE G 313 TRP 0.016 0.003 TRP D 334 Details of bonding type rmsd covalent geometry : bond 0.00309 ( 3744) covalent geometry : angle 0.62514 ( 4980) hydrogen bonds : bond 0.02657 ( 30) hydrogen bonds : angle 5.16530 ( 90) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 156 time to evaluate : 0.130 Fit side-chains REVERT: A 307 MET cc_start: 0.8091 (ttm) cc_final: 0.7891 (ttt) REVERT: A 336 MET cc_start: 0.7483 (ttt) cc_final: 0.7149 (ttt) REVERT: B 336 MET cc_start: 0.7485 (ttt) cc_final: 0.7151 (ttt) REVERT: C 322 MET cc_start: 0.7274 (mtt) cc_final: 0.6886 (mtt) REVERT: C 346 GLN cc_start: 0.7717 (mm-40) cc_final: 0.7436 (mm-40) REVERT: D 322 MET cc_start: 0.7264 (mtt) cc_final: 0.6854 (mtt) REVERT: D 346 GLN cc_start: 0.7730 (OUTLIER) cc_final: 0.7457 (mm-40) REVERT: E 322 MET cc_start: 0.7800 (mpp) cc_final: 0.7169 (mmm) REVERT: F 322 MET cc_start: 0.7800 (mpp) cc_final: 0.7175 (mmm) REVERT: G 322 MET cc_start: 0.7336 (mtt) cc_final: 0.6658 (mtt) REVERT: H 322 MET cc_start: 0.7322 (mtt) cc_final: 0.6649 (mtt) REVERT: I 336 MET cc_start: 0.7567 (ttt) cc_final: 0.7349 (tmm) REVERT: I 337 MET cc_start: 0.7373 (mtp) cc_final: 0.6905 (mtp) REVERT: J 336 MET cc_start: 0.7567 (ttt) cc_final: 0.7342 (tmm) REVERT: J 337 MET cc_start: 0.7382 (mtp) cc_final: 0.6908 (mtp) REVERT: K 322 MET cc_start: 0.7892 (mpp) cc_final: 0.7519 (mtt) REVERT: L 322 MET cc_start: 0.7890 (mpp) cc_final: 0.7525 (mtt) outliers start: 7 outliers final: 2 residues processed: 156 average time/residue: 0.0516 time to fit residues: 10.4986 Evaluate side-chains 147 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 144 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain I residue 345 ASN Chi-restraints excluded: chain J residue 345 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 43 optimal weight: 0.5980 chunk 37 optimal weight: 3.9990 chunk 5 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 16 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 44 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 24 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 15 optimal weight: 8.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN D 346 GLN ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN H 346 GLN ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5260 r_free = 0.5260 target = 0.389497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.5593 r_free = 0.5593 target = 0.284942 restraints weight = 4981.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.5547 r_free = 0.5547 target = 0.287305 restraints weight = 6401.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.5555 r_free = 0.5555 target = 0.288417 restraints weight = 5912.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.5556 r_free = 0.5556 target = 0.288982 restraints weight = 4987.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.5559 r_free = 0.5559 target = 0.289491 restraints weight = 4746.834| |-----------------------------------------------------------------------------| r_work (final): 0.5094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7158 moved from start: 0.4672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3744 Z= 0.132 Angle : 0.640 6.528 4980 Z= 0.332 Chirality : 0.039 0.110 480 Planarity : 0.002 0.010 684 Dihedral : 5.427 17.520 528 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.87 % Allowed : 26.15 % Favored : 70.98 % 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: -4.53 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.45 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.012 0.002 PHE G 313 TRP 0.022 0.004 TRP C 334 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 3744) covalent geometry : angle 0.64029 ( 4980) hydrogen bonds : bond 0.02164 ( 30) hydrogen bonds : angle 5.57257 ( 90) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 150 time to evaluate : 0.139 Fit side-chains REVERT: A 307 MET cc_start: 0.8121 (ttm) cc_final: 0.7880 (ttt) REVERT: A 336 MET cc_start: 0.7444 (ttt) cc_final: 0.7176 (ttt) REVERT: B 336 MET cc_start: 0.7391 (ttt) cc_final: 0.7138 (ttt) REVERT: C 322 MET cc_start: 0.7246 (mtt) cc_final: 0.6662 (mtt) REVERT: D 322 MET cc_start: 0.7106 (mtt) cc_final: 0.6535 (mtt) REVERT: E 346 GLN cc_start: 0.7960 (mm-40) cc_final: 0.7669 (mm-40) REVERT: F 346 GLN cc_start: 0.8027 (mm-40) cc_final: 0.7715 (mm-40) REVERT: G 322 MET cc_start: 0.7030 (mtt) cc_final: 0.6661 (mtt) REVERT: G 346 GLN cc_start: 0.8081 (OUTLIER) cc_final: 0.7878 (mm-40) REVERT: H 322 MET cc_start: 0.7030 (mtt) cc_final: 0.6669 (mtt) REVERT: I 336 MET cc_start: 0.7705 (OUTLIER) cc_final: 0.7345 (ttt) REVERT: J 336 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7332 (ttt) REVERT: K 322 MET cc_start: 0.7867 (mpp) cc_final: 0.7596 (mtt) REVERT: L 322 MET cc_start: 0.7878 (mpp) cc_final: 0.7614 (mtt) outliers start: 10 outliers final: 3 residues processed: 150 average time/residue: 0.0499 time to fit residues: 9.8635 Evaluate side-chains 144 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 138 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 322 MET Chi-restraints excluded: chain B residue 322 MET Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain J residue 336 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 0.0370 chunk 39 optimal weight: 6.9990 chunk 27 optimal weight: 0.9990 chunk 14 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 45 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 overall best weight: 1.5664 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN D 327 GLN D 346 GLN ** E 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 346 GLN H 346 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.384186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.5678 r_free = 0.5678 target = 0.274435 restraints weight = 5024.972| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.5685 r_free = 0.5685 target = 0.275940 restraints weight = 4226.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.5689 r_free = 0.5689 target = 0.276520 restraints weight = 3800.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5689 r_free = 0.5689 target = 0.276520 restraints weight = 3579.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5689 r_free = 0.5689 target = 0.276520 restraints weight = 3579.032| |-----------------------------------------------------------------------------| r_work (final): 0.5079 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7183 moved from start: 0.5312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 3744 Z= 0.188 Angle : 0.707 7.396 4980 Z= 0.370 Chirality : 0.040 0.110 480 Planarity : 0.002 0.010 684 Dihedral : 5.539 18.688 528 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.52 % Favored : 97.48 % Rotamer: Outliers : 3.74 % Allowed : 27.87 % Favored : 68.39 % 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: -4.51 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE H 313 TRP 0.025 0.004 TRP D 334 Details of bonding type rmsd covalent geometry : bond 0.00411 ( 3744) covalent geometry : angle 0.70716 ( 4980) hydrogen bonds : bond 0.02704 ( 30) hydrogen bonds : angle 5.24158 ( 90) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 142 time to evaluate : 0.129 Fit side-chains REVERT: A 307 MET cc_start: 0.8087 (ttm) cc_final: 0.7848 (ttt) REVERT: A 331 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.7874 (pt0) REVERT: A 336 MET cc_start: 0.7739 (ttt) cc_final: 0.7539 (ttt) REVERT: B 331 GLN cc_start: 0.8638 (OUTLIER) cc_final: 0.7929 (pt0) REVERT: C 322 MET cc_start: 0.7197 (mtt) cc_final: 0.6160 (mtt) REVERT: C 343 GLN cc_start: 0.8269 (mp10) cc_final: 0.7987 (mp10) REVERT: D 322 MET cc_start: 0.7304 (mtt) cc_final: 0.6342 (mtt) REVERT: D 343 GLN cc_start: 0.8286 (mp10) cc_final: 0.8028 (mp10) REVERT: E 346 GLN cc_start: 0.7992 (mm-40) cc_final: 0.7768 (mm-40) REVERT: F 346 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7884 (mm-40) REVERT: G 346 GLN cc_start: 0.7850 (mm-40) cc_final: 0.7576 (tp40) REVERT: I 327 GLN cc_start: 0.7287 (tp-100) cc_final: 0.7019 (tp-100) REVERT: I 336 MET cc_start: 0.7843 (OUTLIER) cc_final: 0.7404 (ttt) REVERT: J 327 GLN cc_start: 0.7295 (tp-100) cc_final: 0.7020 (tp-100) REVERT: J 336 MET cc_start: 0.7851 (OUTLIER) cc_final: 0.7411 (ttt) REVERT: K 322 MET cc_start: 0.8065 (mpp) cc_final: 0.7697 (mtt) REVERT: L 322 MET cc_start: 0.8061 (mpp) cc_final: 0.7704 (mtt) outliers start: 13 outliers final: 6 residues processed: 142 average time/residue: 0.0505 time to fit residues: 9.3684 Evaluate side-chains 151 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 140 time to evaluate : 0.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain H residue 346 GLN Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain J residue 336 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 13 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 7 optimal weight: 0.7980 chunk 23 optimal weight: 4.9990 chunk 33 optimal weight: 4.9990 chunk 14 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 327 GLN C 346 GLN E 346 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5224 r_free = 0.5224 target = 0.379728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.5621 r_free = 0.5621 target = 0.268080 restraints weight = 5012.878| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.5625 r_free = 0.5625 target = 0.269019 restraints weight = 4378.935| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5625 r_free = 0.5625 target = 0.269084 restraints weight = 4026.076| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 21)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.269681 restraints weight = 3997.854| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.5627 r_free = 0.5627 target = 0.269692 restraints weight = 3820.024| |-----------------------------------------------------------------------------| r_work (final): 0.5036 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.5617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3744 Z= 0.237 Angle : 0.746 8.364 4980 Z= 0.383 Chirality : 0.040 0.105 480 Planarity : 0.002 0.009 684 Dihedral : 5.654 21.335 528 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 5.17 % Allowed : 25.57 % Favored : 69.25 % 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: -4.59 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.002 PHE H 313 TRP 0.023 0.005 TRP D 334 Details of bonding type rmsd covalent geometry : bond 0.00507 ( 3744) covalent geometry : angle 0.74586 ( 4980) hydrogen bonds : bond 0.03160 ( 30) hydrogen bonds : angle 4.90810 ( 90) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 147 time to evaluate : 0.127 Fit side-chains REVERT: A 307 MET cc_start: 0.8274 (ttm) cc_final: 0.8026 (ttt) REVERT: A 331 GLN cc_start: 0.8659 (OUTLIER) cc_final: 0.8031 (pt0) REVERT: A 336 MET cc_start: 0.7848 (ttt) cc_final: 0.7647 (ttt) REVERT: B 331 GLN cc_start: 0.8662 (OUTLIER) cc_final: 0.8061 (pt0) REVERT: C 322 MET cc_start: 0.7472 (mtt) cc_final: 0.6356 (mtt) REVERT: C 327 GLN cc_start: 0.8005 (OUTLIER) cc_final: 0.7579 (mt0) REVERT: C 343 GLN cc_start: 0.8352 (mp10) cc_final: 0.8112 (mp10) REVERT: C 346 GLN cc_start: 0.7883 (OUTLIER) cc_final: 0.7666 (tp40) REVERT: D 322 MET cc_start: 0.7489 (mtt) cc_final: 0.6413 (mtt) REVERT: D 343 GLN cc_start: 0.8330 (mp10) cc_final: 0.8069 (mp10) REVERT: E 312 ASN cc_start: 0.8289 (t0) cc_final: 0.8045 (t0) REVERT: F 312 ASN cc_start: 0.8280 (t0) cc_final: 0.7977 (t0) REVERT: I 336 MET cc_start: 0.7871 (OUTLIER) cc_final: 0.7668 (ttt) REVERT: K 322 MET cc_start: 0.8051 (mpp) cc_final: 0.7746 (mtt) REVERT: L 322 MET cc_start: 0.8055 (mpp) cc_final: 0.7753 (mtt) outliers start: 18 outliers final: 5 residues processed: 147 average time/residue: 0.0534 time to fit residues: 10.2028 Evaluate side-chains 154 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain C residue 327 GLN Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain L residue 323 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 30 optimal weight: 7.9990 chunk 3 optimal weight: 3.9990 chunk 2 optimal weight: 0.0270 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 8.9990 chunk 23 optimal weight: 0.8980 chunk 46 optimal weight: 0.0970 chunk 26 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 overall best weight: 0.5436 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 327 GLN D 346 GLN E 327 GLN E 346 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5267 r_free = 0.5267 target = 0.392335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.5740 r_free = 0.5740 target = 0.282281 restraints weight = 5077.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5743 r_free = 0.5743 target = 0.283695 restraints weight = 4105.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.5779 r_free = 0.5779 target = 0.286045 restraints weight = 3628.301| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5781 r_free = 0.5781 target = 0.286739 restraints weight = 3252.211| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.5782 r_free = 0.5782 target = 0.286964 restraints weight = 3062.637| |-----------------------------------------------------------------------------| r_work (final): 0.5119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7153 moved from start: 0.5974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3744 Z= 0.127 Angle : 0.669 6.559 4980 Z= 0.338 Chirality : 0.039 0.105 480 Planarity : 0.002 0.012 684 Dihedral : 5.421 18.282 528 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.19 % Favored : 99.81 % Rotamer: Outliers : 4.31 % Allowed : 29.31 % Favored : 66.38 % 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: -4.60 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.50 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE H 313 TRP 0.013 0.003 TRP C 334 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 3744) covalent geometry : angle 0.66880 ( 4980) hydrogen bonds : bond 0.02236 ( 30) hydrogen bonds : angle 4.47047 ( 90) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 151 time to evaluate : 0.127 Fit side-chains REVERT: A 307 MET cc_start: 0.8076 (ttm) cc_final: 0.7842 (ttt) REVERT: A 331 GLN cc_start: 0.8524 (OUTLIER) cc_final: 0.7632 (pt0) REVERT: A 336 MET cc_start: 0.7623 (ttt) cc_final: 0.7224 (ttt) REVERT: B 331 GLN cc_start: 0.8511 (OUTLIER) cc_final: 0.7499 (pt0) REVERT: C 322 MET cc_start: 0.7409 (mtt) cc_final: 0.6484 (mmt) REVERT: C 343 GLN cc_start: 0.8297 (mp10) cc_final: 0.7971 (mp10) REVERT: D 322 MET cc_start: 0.7297 (mtt) cc_final: 0.6382 (mmt) REVERT: D 343 GLN cc_start: 0.8259 (mp10) cc_final: 0.8030 (mp10) REVERT: E 322 MET cc_start: 0.7355 (OUTLIER) cc_final: 0.6990 (mmt) REVERT: F 322 MET cc_start: 0.7328 (OUTLIER) cc_final: 0.7039 (mmt) REVERT: G 312 ASN cc_start: 0.7697 (t0) cc_final: 0.7301 (t0) REVERT: H 312 ASN cc_start: 0.7688 (t0) cc_final: 0.7257 (t0) REVERT: H 343 GLN cc_start: 0.8373 (mp10) cc_final: 0.8120 (mp10) REVERT: K 312 ASN cc_start: 0.7586 (t0) cc_final: 0.6979 (t0) REVERT: K 322 MET cc_start: 0.8003 (mpp) cc_final: 0.7716 (mtt) REVERT: L 322 MET cc_start: 0.8006 (mpp) cc_final: 0.7717 (mtt) outliers start: 15 outliers final: 6 residues processed: 151 average time/residue: 0.0507 time to fit residues: 9.9936 Evaluate side-chains 157 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 147 time to evaluate : 0.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain D residue 327 GLN Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain H residue 323 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 8 optimal weight: 0.0870 chunk 29 optimal weight: 5.9990 chunk 30 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 15 optimal weight: 6.9990 chunk 41 optimal weight: 3.9990 chunk 18 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** 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 = 0.5210 r_free = 0.5210 target = 0.385872 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 79)----------------| | r_work = 0.5698 r_free = 0.5698 target = 0.268556 restraints weight = 5372.691| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.5700 r_free = 0.5700 target = 0.270017 restraints weight = 4603.046| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5743 r_free = 0.5743 target = 0.271682 restraints weight = 4117.872| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.5744 r_free = 0.5744 target = 0.271941 restraints weight = 3826.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5744 r_free = 0.5744 target = 0.271941 restraints weight = 3725.440| |-----------------------------------------------------------------------------| r_work (final): 0.5048 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.6270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.036 3744 Z= 0.268 Angle : 0.854 8.606 4980 Z= 0.435 Chirality : 0.042 0.127 480 Planarity : 0.003 0.010 684 Dihedral : 5.892 23.196 528 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 4.60 % Allowed : 31.61 % Favored : 63.79 % 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: -4.68 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE H 313 TRP 0.022 0.005 TRP D 334 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 3744) covalent geometry : angle 0.85424 ( 4980) hydrogen bonds : bond 0.03362 ( 30) hydrogen bonds : angle 4.80028 ( 90) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 149 time to evaluate : 0.092 Fit side-chains REVERT: A 307 MET cc_start: 0.8472 (ttm) cc_final: 0.8183 (ttt) REVERT: A 331 GLN cc_start: 0.8642 (OUTLIER) cc_final: 0.8177 (pt0) REVERT: A 336 MET cc_start: 0.7770 (ttt) cc_final: 0.7539 (ttt) REVERT: B 331 GLN cc_start: 0.8637 (OUTLIER) cc_final: 0.8187 (pt0) REVERT: C 322 MET cc_start: 0.7549 (mtt) cc_final: 0.6637 (mtt) REVERT: C 343 GLN cc_start: 0.8214 (mp10) cc_final: 0.7899 (mp10) REVERT: D 322 MET cc_start: 0.7570 (mtt) cc_final: 0.6719 (mtt) REVERT: D 343 GLN cc_start: 0.8286 (mp10) cc_final: 0.7985 (mp10) REVERT: E 322 MET cc_start: 0.7367 (OUTLIER) cc_final: 0.7053 (mtt) REVERT: F 322 MET cc_start: 0.7363 (OUTLIER) cc_final: 0.7023 (mtt) REVERT: H 343 GLN cc_start: 0.8360 (mp10) cc_final: 0.8104 (mp10) REVERT: K 312 ASN cc_start: 0.7459 (t0) cc_final: 0.7140 (t0) REVERT: K 322 MET cc_start: 0.8091 (mpp) cc_final: 0.7705 (mpp) REVERT: K 346 GLN cc_start: 0.6463 (mm110) cc_final: 0.6019 (mm-40) REVERT: L 322 MET cc_start: 0.8095 (mpp) cc_final: 0.7702 (mpp) REVERT: L 346 GLN cc_start: 0.6494 (mm110) cc_final: 0.5994 (mm-40) outliers start: 16 outliers final: 5 residues processed: 149 average time/residue: 0.0489 time to fit residues: 9.5584 Evaluate side-chains 156 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 147 time to evaluate : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 5.9990 chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 27 optimal weight: 0.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 346 GLN ** 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 = 0.5265 r_free = 0.5265 target = 0.396950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 77)----------------| | r_work = 0.5792 r_free = 0.5792 target = 0.283677 restraints weight = 5304.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5795 r_free = 0.5795 target = 0.285155 restraints weight = 4501.752| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.5797 r_free = 0.5797 target = 0.286483 restraints weight = 4014.910| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 22)----------------| | r_work = 0.5797 r_free = 0.5797 target = 0.286488 restraints weight = 3679.143| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5797 r_free = 0.5797 target = 0.286488 restraints weight = 3677.103| |-----------------------------------------------------------------------------| r_work (final): 0.5098 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.6550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3744 Z= 0.158 Angle : 0.762 7.947 4980 Z= 0.382 Chirality : 0.039 0.103 480 Planarity : 0.002 0.012 684 Dihedral : 5.683 24.169 528 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.02 % Allowed : 31.61 % Favored : 64.37 % 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: -4.66 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.014 0.002 PHE H 313 TRP 0.014 0.003 TRP E 334 Details of bonding type rmsd covalent geometry : bond 0.00356 ( 3744) covalent geometry : angle 0.76244 ( 4980) hydrogen bonds : bond 0.02447 ( 30) hydrogen bonds : angle 4.67487 ( 90) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.143 Fit side-chains REVERT: A 307 MET cc_start: 0.8135 (ttm) cc_final: 0.7881 (ttt) REVERT: A 331 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.7741 (pt0) REVERT: B 331 GLN cc_start: 0.8525 (OUTLIER) cc_final: 0.7959 (pt0) REVERT: C 322 MET cc_start: 0.7452 (mtt) cc_final: 0.6744 (mmt) REVERT: C 343 GLN cc_start: 0.8246 (mp10) cc_final: 0.7958 (mp10) REVERT: C 346 GLN cc_start: 0.8040 (tp40) cc_final: 0.7775 (tp40) REVERT: D 322 MET cc_start: 0.7383 (mtt) cc_final: 0.6241 (mtt) REVERT: D 337 MET cc_start: 0.7631 (mtp) cc_final: 0.7282 (mtp) REVERT: D 343 GLN cc_start: 0.8214 (mp10) cc_final: 0.7932 (mp10) REVERT: E 322 MET cc_start: 0.7388 (OUTLIER) cc_final: 0.6950 (mtt) REVERT: F 322 MET cc_start: 0.7382 (OUTLIER) cc_final: 0.6990 (mmt) REVERT: G 343 GLN cc_start: 0.8284 (mp10) cc_final: 0.8076 (mp10) REVERT: H 343 GLN cc_start: 0.8295 (mp10) cc_final: 0.8006 (mp10) REVERT: K 322 MET cc_start: 0.7992 (mpp) cc_final: 0.7614 (mpp) REVERT: L 322 MET cc_start: 0.8001 (mpp) cc_final: 0.7616 (mpp) outliers start: 14 outliers final: 4 residues processed: 151 average time/residue: 0.0472 time to fit residues: 9.3593 Evaluate side-chains 156 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 148 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 12 optimal weight: 7.9990 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 0.9990 chunk 19 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 30 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 39 optimal weight: 5.9990 chunk 41 optimal weight: 0.8980 chunk 2 optimal weight: 7.9990 overall best weight: 2.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 344 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 344 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5210 r_free = 0.5210 target = 0.382477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 82)----------------| | r_work = 0.5679 r_free = 0.5679 target = 0.263014 restraints weight = 5281.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.5681 r_free = 0.5681 target = 0.264020 restraints weight = 4751.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 22)----------------| | r_work = 0.5681 r_free = 0.5681 target = 0.264020 restraints weight = 4405.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 17)----------------| | r_work = 0.5681 r_free = 0.5681 target = 0.264021 restraints weight = 4405.138| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5681 r_free = 0.5681 target = 0.264021 restraints weight = 4404.805| |-----------------------------------------------------------------------------| r_work (final): 0.5016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7406 moved from start: 0.6775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 3744 Z= 0.304 Angle : 0.924 9.640 4980 Z= 0.468 Chirality : 0.043 0.119 480 Planarity : 0.003 0.010 684 Dihedral : 6.225 23.904 528 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 16.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 4.02 % Allowed : 32.18 % Favored : 63.79 % 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: -4.81 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.66 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.013 0.003 PHE G 313 TRP 0.025 0.006 TRP G 334 Details of bonding type rmsd covalent geometry : bond 0.00645 ( 3744) covalent geometry : angle 0.92372 ( 4980) hydrogen bonds : bond 0.03716 ( 30) hydrogen bonds : angle 4.76057 ( 90) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 151 time to evaluate : 0.139 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8473 (ttm) cc_final: 0.8145 (ttt) REVERT: A 331 GLN cc_start: 0.8736 (OUTLIER) cc_final: 0.8169 (pt0) REVERT: B 331 GLN cc_start: 0.8737 (OUTLIER) cc_final: 0.8219 (pt0) REVERT: B 337 MET cc_start: 0.8126 (OUTLIER) cc_final: 0.7917 (mtt) REVERT: C 322 MET cc_start: 0.7565 (mtt) cc_final: 0.6670 (mtt) REVERT: C 336 MET cc_start: 0.8052 (ttp) cc_final: 0.7820 (ttm) REVERT: C 343 GLN cc_start: 0.8263 (mp10) cc_final: 0.7966 (mp10) REVERT: D 322 MET cc_start: 0.7677 (mtt) cc_final: 0.6921 (mtt) REVERT: D 337 MET cc_start: 0.7988 (mtp) cc_final: 0.7508 (mtp) REVERT: D 343 GLN cc_start: 0.8258 (mp10) cc_final: 0.7969 (mp10) REVERT: E 322 MET cc_start: 0.7451 (OUTLIER) cc_final: 0.7157 (mtt) REVERT: F 322 MET cc_start: 0.7325 (OUTLIER) cc_final: 0.6983 (mtt) REVERT: G 343 GLN cc_start: 0.8278 (mp10) cc_final: 0.7978 (mp10) REVERT: H 343 GLN cc_start: 0.8282 (mp10) cc_final: 0.8006 (mp10) REVERT: K 322 MET cc_start: 0.8096 (mpp) cc_final: 0.7736 (mpp) REVERT: L 322 MET cc_start: 0.8115 (mpp) cc_final: 0.7790 (mpp) outliers start: 14 outliers final: 7 residues processed: 151 average time/residue: 0.0493 time to fit residues: 9.7748 Evaluate side-chains 158 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 146 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain L residue 323 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 19 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 6.9990 chunk 44 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 22 optimal weight: 9.9990 chunk 28 optimal weight: 4.9990 chunk 42 optimal weight: 0.0270 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5253 r_free = 0.5253 target = 0.394290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.5779 r_free = 0.5779 target = 0.279296 restraints weight = 5398.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5786 r_free = 0.5786 target = 0.281031 restraints weight = 4676.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.5828 r_free = 0.5828 target = 0.282409 restraints weight = 4232.201| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.5830 r_free = 0.5830 target = 0.282894 restraints weight = 3956.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5830 r_free = 0.5830 target = 0.283182 restraints weight = 3793.108| |-----------------------------------------------------------------------------| r_work (final): 0.5096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 moved from start: 0.6946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3744 Z= 0.164 Angle : 0.805 7.981 4980 Z= 0.403 Chirality : 0.040 0.105 480 Planarity : 0.002 0.011 684 Dihedral : 5.792 21.874 528 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 3.74 % Allowed : 31.61 % Favored : 64.66 % 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: -4.73 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.60 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE H 313 TRP 0.016 0.003 TRP G 334 Details of bonding type rmsd covalent geometry : bond 0.00375 ( 3744) covalent geometry : angle 0.80505 ( 4980) hydrogen bonds : bond 0.02894 ( 30) hydrogen bonds : angle 4.58078 ( 90) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 150 time to evaluate : 0.123 Fit side-chains revert: symmetry clash REVERT: A 307 MET cc_start: 0.8435 (ttm) cc_final: 0.8133 (ttt) REVERT: A 331 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.7700 (pt0) REVERT: B 331 GLN cc_start: 0.8555 (OUTLIER) cc_final: 0.7900 (pt0) REVERT: C 322 MET cc_start: 0.7326 (mtt) cc_final: 0.6716 (mmt) REVERT: C 343 GLN cc_start: 0.8260 (mp10) cc_final: 0.7990 (mp10) REVERT: D 322 MET cc_start: 0.7412 (mtt) cc_final: 0.6872 (mmt) REVERT: D 337 MET cc_start: 0.7582 (mtp) cc_final: 0.7186 (mtp) REVERT: D 343 GLN cc_start: 0.8268 (mp10) cc_final: 0.8019 (mp10) REVERT: E 307 MET cc_start: 0.7762 (ttt) cc_final: 0.7370 (ttt) REVERT: E 322 MET cc_start: 0.7311 (OUTLIER) cc_final: 0.6831 (mtt) REVERT: E 344 GLN cc_start: 0.8671 (mp10) cc_final: 0.8389 (mm-40) REVERT: F 322 MET cc_start: 0.7378 (OUTLIER) cc_final: 0.6843 (mtt) REVERT: G 343 GLN cc_start: 0.8302 (mp10) cc_final: 0.7989 (mp10) REVERT: I 344 GLN cc_start: 0.8437 (mp10) cc_final: 0.8156 (mp10) REVERT: J 344 GLN cc_start: 0.8478 (mp10) cc_final: 0.8156 (mp10) REVERT: K 322 MET cc_start: 0.8026 (mpp) cc_final: 0.7714 (mpp) REVERT: L 322 MET cc_start: 0.8007 (mpp) cc_final: 0.7705 (mpp) outliers start: 13 outliers final: 6 residues processed: 150 average time/residue: 0.0494 time to fit residues: 9.7223 Evaluate side-chains 154 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 144 time to evaluate : 0.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 331 GLN Chi-restraints excluded: chain B residue 331 GLN Chi-restraints excluded: chain B residue 337 MET Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain E residue 322 MET Chi-restraints excluded: chain F residue 322 MET Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN Chi-restraints excluded: chain H residue 323 MET Chi-restraints excluded: chain H residue 344 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 0 optimal weight: 10.0000 chunk 44 optimal weight: 0.6980 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 20 optimal weight: 7.9990 chunk 30 optimal weight: 1.9990 chunk 9 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 331 GLN ** E 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 331 GLN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN H 331 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5256 r_free = 0.5256 target = 0.392428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 74)----------------| | r_work = 0.5763 r_free = 0.5763 target = 0.275802 restraints weight = 5331.950| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.5796 r_free = 0.5796 target = 0.277591 restraints weight = 4759.277| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.5797 r_free = 0.5797 target = 0.277849 restraints weight = 4360.501| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.5798 r_free = 0.5798 target = 0.278063 restraints weight = 4254.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.5797 r_free = 0.5797 target = 0.278065 restraints weight = 4193.169| |-----------------------------------------------------------------------------| r_work (final): 0.5083 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7301 moved from start: 0.7078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3744 Z= 0.181 Angle : 0.832 9.338 4980 Z= 0.416 Chirality : 0.040 0.104 480 Planarity : 0.002 0.011 684 Dihedral : 5.753 21.877 528 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 16.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 3.16 % Allowed : 32.76 % Favored : 64.08 % 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: -4.78 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.64 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile PHE 0.016 0.002 PHE H 313 TRP 0.018 0.003 TRP G 334 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 3744) covalent geometry : angle 0.83229 ( 4980) hydrogen bonds : bond 0.02783 ( 30) hydrogen bonds : angle 4.92742 ( 90) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 862.30 seconds wall clock time: 15 minutes 31.47 seconds (931.47 seconds total)