Starting phenix.real_space_refine on Fri Dec 27 08:51:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qx9_18715/12_2024/8qx9_18715.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qx9_18715/12_2024/8qx9_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/8qx9_18715/12_2024/8qx9_18715.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qx9_18715/12_2024/8qx9_18715.map" model { file = "/net/cci-nas-00/data/ceres_data/8qx9_18715/12_2024/8qx9_18715.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qx9_18715/12_2024/8qx9_18715.cif" } resolution = 3.76 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= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/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: C, B, E, D, G, F, I, H, K, J, L Time building chain proxies: 1.36, per 1000 atoms: 0.37 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: 0.86 Conformation dependent library (CDL) restraints added in 505.9 milliseconds 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: 0.38 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: 0.75 Time building geometry restraints manager: 0.99 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: 0.00 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' } 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: 0.440 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 11.420 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.040 ------------------------------------------------------------------------------- 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= 0.915 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 (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: -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 TRP 0.046 0.010 TRP C 334 PHE 0.012 0.003 PHE L 316 *********************** 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 : 0.397 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: I 337 MET cc_start: 0.7608 (mtp) cc_final: 0.6965 (mtp) REVERT: J 337 MET cc_start: 0.7626 (mtp) cc_final: 0.6969 (mtp) outliers start: 0 outliers final: 0 residues processed: 172 average time/residue: 0.1298 time to fit residues: 28.1699 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 : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 6.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 43 optimal weight: 1.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 319 ASN K 327 GLN L 319 ASN L 327 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6902 moved from start: 0.4150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3744 Z= 0.211 Angle : 0.665 7.790 4980 Z= 0.342 Chirality : 0.039 0.110 480 Planarity : 0.003 0.016 684 Dihedral : 5.747 21.137 528 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 12.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 1.72 % Allowed : 26.15 % Favored : 72.13 % 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: -4.55 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.003 TRP D 334 PHE 0.009 0.003 PHE G 313 *********************** 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 164 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 158 time to evaluate : 0.411 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 336 MET cc_start: 0.7681 (OUTLIER) cc_final: 0.7357 (tmm) REVERT: D 336 MET cc_start: 0.7679 (OUTLIER) cc_final: 0.7360 (tmm) REVERT: I 336 MET cc_start: 0.7983 (OUTLIER) cc_final: 0.7575 (tmm) REVERT: I 337 MET cc_start: 0.7772 (mtp) cc_final: 0.7427 (mtp) REVERT: J 336 MET cc_start: 0.7978 (OUTLIER) cc_final: 0.7589 (tmm) REVERT: J 337 MET cc_start: 0.7776 (mtp) cc_final: 0.7435 (mtp) outliers start: 6 outliers final: 0 residues processed: 158 average time/residue: 0.1292 time to fit residues: 25.8181 Evaluate side-chains 148 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 144 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 336 MET Chi-restraints excluded: chain D residue 336 MET Chi-restraints excluded: chain I residue 336 MET Chi-restraints excluded: chain J residue 336 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 29 optimal weight: 6.9990 chunk 12 optimal weight: 9.9990 chunk 43 optimal weight: 7.9990 chunk 47 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 7.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.4831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3744 Z= 0.223 Angle : 0.654 7.258 4980 Z= 0.337 Chirality : 0.040 0.108 480 Planarity : 0.002 0.011 684 Dihedral : 5.778 20.667 528 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 12.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 4.02 % Allowed : 25.86 % Favored : 70.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -4.43 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP D 334 PHE 0.013 0.002 PHE G 313 *********************** 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 162 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 148 time to evaluate : 0.416 Fit side-chains REVERT: I 307 MET cc_start: 0.8274 (ttm) cc_final: 0.8026 (ttp) REVERT: I 337 MET cc_start: 0.7801 (mtp) cc_final: 0.7478 (mtt) REVERT: J 307 MET cc_start: 0.8267 (ttm) cc_final: 0.8022 (ttp) REVERT: J 337 MET cc_start: 0.7802 (mtp) cc_final: 0.7484 (mtt) outliers start: 14 outliers final: 8 residues processed: 148 average time/residue: 0.1252 time to fit residues: 23.5698 Evaluate side-chains 144 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 136 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain H residue 345 ASN Chi-restraints excluded: chain I residue 345 ASN Chi-restraints excluded: chain J residue 345 ASN Chi-restraints excluded: chain K residue 323 MET Chi-restraints excluded: chain L residue 323 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 10.0000 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 0.8980 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 0.0980 chunk 46 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 12 optimal weight: 8.9990 chunk 38 optimal weight: 0.9990 chunk 26 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 346 GLN E 327 GLN E 346 GLN F 327 GLN F 346 GLN G 346 GLN H 346 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: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7063 moved from start: 0.5412 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= 0.299 Angle : 0.712 8.010 4980 Z= 0.372 Chirality : 0.040 0.111 480 Planarity : 0.002 0.010 684 Dihedral : 5.875 19.771 528 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 4.60 % Allowed : 28.45 % Favored : 66.95 % 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: -4.48 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP D 334 PHE 0.013 0.003 PHE G 313 *********************** 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 162 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 146 time to evaluate : 0.350 Fit side-chains REVERT: C 336 MET cc_start: 0.7458 (tmm) cc_final: 0.7204 (tmm) REVERT: D 336 MET cc_start: 0.7457 (tmm) cc_final: 0.7211 (tmm) REVERT: I 336 MET cc_start: 0.7833 (tmm) cc_final: 0.7366 (tmm) REVERT: I 337 MET cc_start: 0.7928 (mtp) cc_final: 0.7575 (mtp) REVERT: J 336 MET cc_start: 0.7819 (tmm) cc_final: 0.7370 (tmm) REVERT: J 337 MET cc_start: 0.7933 (mtp) cc_final: 0.7583 (mtp) outliers start: 16 outliers final: 11 residues processed: 146 average time/residue: 0.1178 time to fit residues: 21.8501 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 : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain E residue 327 GLN Chi-restraints excluded: chain E residue 346 GLN Chi-restraints excluded: chain F residue 327 GLN Chi-restraints excluded: chain F residue 346 GLN Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain G residue 346 GLN Chi-restraints excluded: chain H residue 345 ASN Chi-restraints excluded: chain H residue 346 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 4.9990 chunk 41 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN I 331 GLN J 331 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.5733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3744 Z= 0.203 Angle : 0.664 7.567 4980 Z= 0.342 Chirality : 0.039 0.107 480 Planarity : 0.002 0.007 684 Dihedral : 5.735 19.582 528 Min Nonbonded Distance : 2.626 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Rotamer: Outliers : 3.45 % Allowed : 30.75 % Favored : 65.80 % 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: -4.47 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.40 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP C 334 PHE 0.013 0.002 PHE G 313 *********************** 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 162 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 150 time to evaluate : 0.393 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 322 MET cc_start: 0.6605 (mtt) cc_final: 0.6301 (mtt) REVERT: C 327 GLN cc_start: 0.5603 (mt0) cc_final: 0.5370 (mt0) REVERT: C 336 MET cc_start: 0.7275 (tmm) cc_final: 0.6916 (tmm) REVERT: D 336 MET cc_start: 0.7277 (tmm) cc_final: 0.6925 (tmm) REVERT: I 307 MET cc_start: 0.8164 (ttm) cc_final: 0.7889 (ttp) REVERT: I 336 MET cc_start: 0.7625 (tmm) cc_final: 0.7173 (tmm) REVERT: J 307 MET cc_start: 0.8158 (ttm) cc_final: 0.7881 (ttp) REVERT: J 336 MET cc_start: 0.7614 (tmm) cc_final: 0.7164 (tmm) outliers start: 12 outliers final: 5 residues processed: 150 average time/residue: 0.1182 time to fit residues: 22.6231 Evaluate side-chains 150 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 145 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain G residue 345 ASN Chi-restraints excluded: chain H residue 345 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 5.9990 chunk 46 optimal weight: 0.0670 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 4.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 2.2126 ------------------------------------------------------------------------------- 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 D 331 GLN F 331 GLN H 331 GLN I 331 GLN J 331 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7130 moved from start: 0.6173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3744 Z= 0.341 Angle : 0.759 7.724 4980 Z= 0.401 Chirality : 0.041 0.105 480 Planarity : 0.002 0.013 684 Dihedral : 6.040 22.016 528 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.71 % Favored : 97.29 % Rotamer: Outliers : 3.16 % Allowed : 33.05 % 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 (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: -4.59 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.005 TRP D 334 PHE 0.013 0.003 PHE H 313 *********************** 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 164 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 153 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 336 MET cc_start: 0.7719 (tmm) cc_final: 0.7047 (tmm) REVERT: D 336 MET cc_start: 0.7714 (tmm) cc_final: 0.7068 (tmm) REVERT: I 307 MET cc_start: 0.8261 (ttm) cc_final: 0.7977 (ttp) REVERT: I 336 MET cc_start: 0.7815 (tmm) cc_final: 0.7237 (tmm) REVERT: J 307 MET cc_start: 0.8247 (ttm) cc_final: 0.7965 (ttp) REVERT: J 336 MET cc_start: 0.7816 (tmm) cc_final: 0.7219 (tmm) outliers start: 11 outliers final: 5 residues processed: 153 average time/residue: 0.1253 time to fit residues: 24.3244 Evaluate side-chains 152 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 147 time to evaluate : 0.414 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain D residue 346 GLN Chi-restraints excluded: chain H residue 344 GLN Chi-restraints excluded: chain I residue 323 MET Chi-restraints excluded: chain J residue 323 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 8.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 9.9990 chunk 28 optimal weight: 7.9990 chunk 21 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 8 optimal weight: 8.9990 overall best weight: 2.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.6543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.028 3744 Z= 0.369 Angle : 0.800 8.137 4980 Z= 0.419 Chirality : 0.041 0.102 480 Planarity : 0.003 0.010 684 Dihedral : 6.276 22.834 528 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 3.74 % Allowed : 31.90 % 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 (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: -4.71 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.58 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.005 TRP D 334 PHE 0.014 0.003 PHE H 313 *********************** 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 164 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 151 time to evaluate : 0.472 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.7399 (OUTLIER) cc_final: 0.6994 (tmt) REVERT: C 336 MET cc_start: 0.7746 (tmm) cc_final: 0.7102 (tmm) REVERT: D 336 MET cc_start: 0.7726 (tmm) cc_final: 0.7253 (tmm) REVERT: I 336 MET cc_start: 0.7894 (tmm) cc_final: 0.7336 (tmm) REVERT: J 336 MET cc_start: 0.7880 (tmm) cc_final: 0.7314 (tmm) outliers start: 13 outliers final: 8 residues processed: 151 average time/residue: 0.1233 time to fit residues: 23.6392 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 : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain C residue 346 GLN Chi-restraints excluded: chain D residue 345 ASN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN 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 29 optimal weight: 2.9990 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 9.9990 chunk 4 optimal weight: 10.0000 chunk 36 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 8.9990 chunk 43 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 18 optimal weight: 8.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN D 331 GLN F 331 GLN H 331 GLN ** K 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7226 moved from start: 0.6820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.037 3744 Z= 0.422 Angle : 0.862 11.774 4980 Z= 0.451 Chirality : 0.043 0.119 480 Planarity : 0.003 0.013 684 Dihedral : 6.651 28.663 528 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.16 % Allowed : 34.77 % Favored : 62.07 % 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: -4.69 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.006 TRP C 334 PHE 0.013 0.003 PHE G 313 *********************** 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 161 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 150 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 336 MET cc_start: 0.7485 (OUTLIER) cc_final: 0.7052 (tmt) REVERT: C 312 ASN cc_start: 0.7757 (t0) cc_final: 0.7502 (t0) REVERT: C 336 MET cc_start: 0.7772 (tmm) cc_final: 0.7134 (tmm) REVERT: D 336 MET cc_start: 0.7746 (tmm) cc_final: 0.7358 (tmm) REVERT: I 336 MET cc_start: 0.7905 (tmm) cc_final: 0.7342 (tmm) REVERT: J 336 MET cc_start: 0.7881 (tmm) cc_final: 0.7311 (tmm) REVERT: K 322 MET cc_start: 0.7403 (mtt) cc_final: 0.7156 (mtt) REVERT: L 322 MET cc_start: 0.7398 (mtt) cc_final: 0.7173 (mtt) REVERT: L 346 GLN cc_start: 0.4634 (mm110) cc_final: 0.4314 (mm-40) outliers start: 11 outliers final: 6 residues processed: 150 average time/residue: 0.1216 time to fit residues: 23.1741 Evaluate side-chains 154 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 147 time to evaluate : 0.351 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 336 MET Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain C residue 323 MET 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 G residue 344 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 45 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 344 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.7007 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= 0.241 Angle : 0.751 8.821 4980 Z= 0.390 Chirality : 0.041 0.105 480 Planarity : 0.002 0.011 684 Dihedral : 6.213 25.052 528 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 14.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 3.16 % Allowed : 33.33 % Favored : 63.51 % 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: -4.63 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP H 334 PHE 0.015 0.002 PHE G 313 *********************** 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 163 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 152 time to evaluate : 0.413 Fit side-chains REVERT: C 312 ASN cc_start: 0.7597 (t0) cc_final: 0.7293 (t0) REVERT: C 336 MET cc_start: 0.7064 (tmm) cc_final: 0.6849 (tmm) REVERT: D 336 MET cc_start: 0.7137 (tmm) cc_final: 0.6810 (tmm) outliers start: 11 outliers final: 5 residues processed: 152 average time/residue: 0.1309 time to fit residues: 25.3818 Evaluate side-chains 148 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 143 time to evaluate : 0.327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASN 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 G residue 344 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 2.9990 chunk 38 optimal weight: 7.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 10 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 344 GLN G 344 GLN 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.7108 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3744 Z= 0.335 Angle : 0.835 10.332 4980 Z= 0.430 Chirality : 0.042 0.107 480 Planarity : 0.002 0.012 684 Dihedral : 6.433 27.845 528 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.59 % Allowed : 33.33 % 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 (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: -4.76 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP J 334 PHE 0.012 0.002 PHE F 313 ********************** 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 155 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 146 time to evaluate : 0.359 Fit side-chains REVERT: D 336 MET cc_start: 0.7468 (tmm) cc_final: 0.7019 (tmm) REVERT: J 337 MET cc_start: 0.8352 (mtp) cc_final: 0.8098 (mmm) outliers start: 9 outliers final: 6 residues processed: 146 average time/residue: 0.1143 time to fit residues: 21.2387 Evaluate side-chains 147 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 141 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 345 ASN Chi-restraints excluded: chain C residue 323 MET Chi-restraints excluded: chain C residue 345 ASN Chi-restraints excluded: chain G residue 323 MET Chi-restraints excluded: chain G residue 344 GLN 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 38 optimal weight: 5.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 0.8980 chunk 4 optimal weight: 10.0000 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 5.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 331 GLN E 331 GLN G 331 GLN G 344 GLN 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: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.5271 r_free = 0.5271 target = 0.410560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.5803 r_free = 0.5803 target = 0.290732 restraints weight = 5587.921| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.5805 r_free = 0.5805 target = 0.292005 restraints weight = 5051.072| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.5849 r_free = 0.5849 target = 0.293403 restraints weight = 4642.686| |-----------------------------------------------------------------------------| r_work (final): 0.5080 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7292 moved from start: 0.7334 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= 0.269 Angle : 0.799 8.909 4980 Z= 0.409 Chirality : 0.041 0.107 480 Planarity : 0.002 0.012 684 Dihedral : 6.315 25.980 528 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 16.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer: Outliers : 2.87 % Allowed : 35.34 % Favored : 61.78 % 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: -4.76 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP G 334 PHE 0.016 0.002 PHE G 313 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1244.30 seconds wall clock time: 23 minutes 4.86 seconds (1384.86 seconds total)