Starting phenix.real_space_refine on Thu Dec 7 16:13:56 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol5_16949/12_2023/8ol5_16949.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol5_16949/12_2023/8ol5_16949.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol5_16949/12_2023/8ol5_16949.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol5_16949/12_2023/8ol5_16949.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol5_16949/12_2023/8ol5_16949.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ol5_16949/12_2023/8ol5_16949.pdb" } resolution = 3.4 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= 1.000 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 10 5.16 5 C 1470 2.51 5 N 390 2.21 5 O 390 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2260 Number of models: 1 Model: "" Number of chains: 10 Chain: "H" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "E" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "A" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "B" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "C" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "D" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "G" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "I" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Chain: "J" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 31, 226 Classifications: {'peptide': 31} Modifications used: {'COO': 1} Link IDs: {'TRANS': 30} Time building chain proxies: 1.59, per 1000 atoms: 0.70 Number of scatterers: 2260 At special positions: 0 Unit cell: (79.992, 54.136, 41.208, 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 10 16.00 O 390 8.00 N 390 7.00 C 1470 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 - 3.50 Amino acid : False - 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: 0.72 Conformation dependent library (CDL) restraints added in 431.3 milliseconds 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 520 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 45.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 14 through 15 removed outlier: 6.368A pdb=" N HIS B 14 " --> pdb=" O GLN D 15 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS D 14 " --> pdb=" O GLN F 15 " (cutoff:3.500A) removed outlier: 6.330A pdb=" N HIS H 14 " --> pdb=" O GLN J 15 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 18 through 20 removed outlier: 6.447A pdb=" N VAL B 18 " --> pdb=" O PHE D 19 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL D 18 " --> pdb=" O PHE F 19 " (cutoff:3.500A) removed outlier: 6.459A pdb=" N VAL H 18 " --> pdb=" O PHE J 19 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 24 through 27 removed outlier: 8.611A pdb=" N VAL B 24 " --> pdb=" O GLY D 25 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN D 27 " --> pdb=" O VAL B 24 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N SER B 26 " --> pdb=" O ASN D 27 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL D 24 " --> pdb=" O GLY F 25 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN F 27 " --> pdb=" O VAL D 24 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N SER D 26 " --> pdb=" O ASN F 27 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N SER F 26 " --> pdb=" O GLY H 25 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N ASN H 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 8.640A pdb=" N VAL H 24 " --> pdb=" O GLY J 25 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N ASN J 27 " --> pdb=" O VAL H 24 " (cutoff:3.500A) removed outlier: 8.982A pdb=" N SER H 26 " --> pdb=" O ASN J 27 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 30 through 36 removed outlier: 6.881A pdb=" N LEU D 34 " --> pdb=" O GLY B 33 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET B 35 " --> pdb=" O LEU D 34 " (cutoff:3.500A) removed outlier: 7.063A pdb=" N VAL D 36 " --> pdb=" O MET B 35 " (cutoff:3.500A) removed outlier: 6.881A pdb=" N LEU F 34 " --> pdb=" O GLY D 33 " (cutoff:3.500A) removed outlier: 7.036A pdb=" N MET D 35 " --> pdb=" O LEU F 34 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL F 36 " --> pdb=" O MET D 35 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N ALA H 30 " --> pdb=" O ILE F 31 " (cutoff:3.500A) removed outlier: 7.852A pdb=" N GLY F 33 " --> pdb=" O ALA H 30 " (cutoff:3.500A) removed outlier: 8.986A pdb=" N ILE H 32 " --> pdb=" O GLY F 33 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N MET F 35 " --> pdb=" O ILE H 32 " (cutoff:3.500A) removed outlier: 9.130A pdb=" N LEU H 34 " --> pdb=" O MET F 35 " (cutoff:3.500A) removed outlier: 6.159A pdb=" N ILE H 31 " --> pdb=" O ILE J 32 " (cutoff:3.500A) removed outlier: 7.002A pdb=" N LEU J 34 " --> pdb=" O ILE H 31 " (cutoff:3.500A) removed outlier: 7.430A pdb=" N GLY H 33 " --> pdb=" O LEU J 34 " (cutoff:3.500A) removed outlier: 10.303A pdb=" N VAL J 36 " --> pdb=" O GLY H 33 " (cutoff:3.500A) removed outlier: 8.880A pdb=" N MET H 35 " --> pdb=" O VAL J 36 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 39 through 41 Processing sheet with id=AA6, first strand: chain 'A' and resid 14 through 15 removed outlier: 6.418A pdb=" N HIS A 14 " --> pdb=" O GLN C 15 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS E 14 " --> pdb=" O GLN G 15 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N HIS G 14 " --> pdb=" O GLN I 15 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 18 through 20 removed outlier: 6.526A pdb=" N VAL A 18 " --> pdb=" O PHE C 19 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL E 18 " --> pdb=" O PHE G 19 " (cutoff:3.500A) removed outlier: 6.446A pdb=" N VAL G 18 " --> pdb=" O PHE I 19 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 24 through 27 removed outlier: 8.630A pdb=" N VAL A 24 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 7.531A pdb=" N ASN C 27 " --> pdb=" O VAL A 24 " (cutoff:3.500A) removed outlier: 8.956A pdb=" N SER A 26 " --> pdb=" O ASN C 27 " (cutoff:3.500A) removed outlier: 6.758A pdb=" N SER C 26 " --> pdb=" O GLY E 25 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASN E 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 8.611A pdb=" N VAL E 24 " --> pdb=" O GLY G 25 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN G 27 " --> pdb=" O VAL E 24 " (cutoff:3.500A) removed outlier: 8.995A pdb=" N SER E 26 " --> pdb=" O ASN G 27 " (cutoff:3.500A) removed outlier: 8.612A pdb=" N VAL G 24 " --> pdb=" O GLY I 25 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ASN I 27 " --> pdb=" O VAL G 24 " (cutoff:3.500A) removed outlier: 8.996A pdb=" N SER G 26 " --> pdb=" O ASN I 27 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 30 through 36 removed outlier: 6.200A pdb=" N ILE A 31 " --> pdb=" O ILE C 32 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N LEU C 34 " --> pdb=" O ILE A 31 " (cutoff:3.500A) removed outlier: 7.386A pdb=" N GLY A 33 " --> pdb=" O LEU C 34 " (cutoff:3.500A) removed outlier: 10.209A pdb=" N VAL C 36 " --> pdb=" O GLY A 33 " (cutoff:3.500A) removed outlier: 8.794A pdb=" N MET A 35 " --> pdb=" O VAL C 36 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N ALA E 30 " --> pdb=" O ILE C 31 " (cutoff:3.500A) removed outlier: 7.914A pdb=" N GLY C 33 " --> pdb=" O ALA E 30 " (cutoff:3.500A) removed outlier: 9.011A pdb=" N ILE E 32 " --> pdb=" O GLY C 33 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N MET C 35 " --> pdb=" O ILE E 32 " (cutoff:3.500A) removed outlier: 9.084A pdb=" N LEU E 34 " --> pdb=" O MET C 35 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU G 34 " --> pdb=" O GLY E 33 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET E 35 " --> pdb=" O LEU G 34 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL G 36 " --> pdb=" O MET E 35 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N LEU I 34 " --> pdb=" O GLY G 33 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N MET G 35 " --> pdb=" O LEU I 34 " (cutoff:3.500A) removed outlier: 7.064A pdb=" N VAL I 36 " --> pdb=" O MET G 35 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 39 through 41 removed outlier: 6.441A pdb=" N VAL E 40 " --> pdb=" O ILE C 41 " (cutoff:3.500A) 34 hydrogen bonds defined for protein. 102 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: 0.52 Time building geometry restraints manager: 0.81 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 740 1.34 - 1.46: 285 1.46 - 1.57: 1245 1.57 - 1.68: 0 1.68 - 1.80: 20 Bond restraints: 2290 Sorted by residual: bond pdb=" CA GLY D 37 " pdb=" C GLY D 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 4.00e-01 bond pdb=" CA GLY A 37 " pdb=" C GLY A 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 3.99e-01 bond pdb=" CA GLY G 37 " pdb=" C GLY G 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 3.75e-01 bond pdb=" CA GLY H 37 " pdb=" C GLY H 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 3.69e-01 bond pdb=" CA GLY E 37 " pdb=" C GLY E 37 " ideal model delta sigma weight residual 1.520 1.512 0.008 1.28e-02 6.10e+03 3.58e-01 ... (remaining 2285 not shown) Histogram of bond angle deviations from ideal: 100.87 - 106.94: 31 106.94 - 113.02: 1329 113.02 - 119.09: 559 119.09 - 125.16: 1141 125.16 - 131.24: 20 Bond angle restraints: 3080 Sorted by residual: angle pdb=" C GLN H 15 " pdb=" N LYS H 16 " pdb=" CA LYS H 16 " ideal model delta sigma weight residual 122.34 124.17 -1.83 1.39e+00 5.18e-01 1.73e+00 angle pdb=" C GLN E 15 " pdb=" N LYS E 16 " pdb=" CA LYS E 16 " ideal model delta sigma weight residual 122.34 124.17 -1.83 1.39e+00 5.18e-01 1.73e+00 angle pdb=" C GLN I 15 " pdb=" N LYS I 16 " pdb=" CA LYS I 16 " ideal model delta sigma weight residual 122.34 124.14 -1.80 1.39e+00 5.18e-01 1.68e+00 angle pdb=" C GLN J 15 " pdb=" N LYS J 16 " pdb=" CA LYS J 16 " ideal model delta sigma weight residual 122.34 124.13 -1.79 1.39e+00 5.18e-01 1.65e+00 angle pdb=" C GLN C 15 " pdb=" N LYS C 16 " pdb=" CA LYS C 16 " ideal model delta sigma weight residual 122.34 124.12 -1.78 1.39e+00 5.18e-01 1.63e+00 ... (remaining 3075 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.65: 1140 8.65 - 17.30: 70 17.30 - 25.95: 50 25.95 - 34.60: 20 34.60 - 43.25: 10 Dihedral angle restraints: 1290 sinusoidal: 470 harmonic: 820 Sorted by residual: dihedral pdb=" CA MET J 35 " pdb=" CB MET J 35 " pdb=" CG MET J 35 " pdb=" SD MET J 35 " ideal model delta sinusoidal sigma weight residual 60.00 103.25 -43.25 3 1.50e+01 4.44e-03 7.77e+00 dihedral pdb=" CA MET D 35 " pdb=" CB MET D 35 " pdb=" CG MET D 35 " pdb=" SD MET D 35 " ideal model delta sinusoidal sigma weight residual 60.00 103.25 -43.25 3 1.50e+01 4.44e-03 7.77e+00 dihedral pdb=" CA MET I 35 " pdb=" CB MET I 35 " pdb=" CG MET I 35 " pdb=" SD MET I 35 " ideal model delta sinusoidal sigma weight residual 60.00 103.24 -43.24 3 1.50e+01 4.44e-03 7.77e+00 ... (remaining 1287 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.024: 156 0.024 - 0.047: 85 0.047 - 0.070: 39 0.070 - 0.093: 8 0.093 - 0.116: 82 Chirality restraints: 370 Sorted by residual: chirality pdb=" CA ILE B 31 " pdb=" N ILE B 31 " pdb=" C ILE B 31 " pdb=" CB ILE B 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.39e-01 chirality pdb=" CA ILE D 31 " pdb=" N ILE D 31 " pdb=" C ILE D 31 " pdb=" CB ILE D 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.31e-01 chirality pdb=" CA ILE H 31 " pdb=" N ILE H 31 " pdb=" C ILE H 31 " pdb=" CB ILE H 31 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.31e-01 ... (remaining 367 not shown) Planarity restraints: 390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 16 " 0.004 2.00e-02 2.50e+03 7.62e-03 5.81e-01 pdb=" C LYS G 16 " -0.013 2.00e-02 2.50e+03 pdb=" O LYS G 16 " 0.005 2.00e-02 2.50e+03 pdb=" N LEU G 17 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 16 " -0.004 2.00e-02 2.50e+03 7.58e-03 5.74e-01 pdb=" C LYS F 16 " 0.013 2.00e-02 2.50e+03 pdb=" O LYS F 16 " -0.005 2.00e-02 2.50e+03 pdb=" N LEU F 17 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 16 " 0.004 2.00e-02 2.50e+03 7.54e-03 5.68e-01 pdb=" C LYS E 16 " -0.013 2.00e-02 2.50e+03 pdb=" O LYS E 16 " 0.005 2.00e-02 2.50e+03 pdb=" N LEU E 17 " 0.004 2.00e-02 2.50e+03 ... (remaining 387 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 824 2.89 - 3.40: 1710 3.40 - 3.90: 4030 3.90 - 4.40: 3993 4.40 - 4.90: 7617 Nonbonded interactions: 18174 Sorted by model distance: nonbonded pdb=" NZ LYS B 28 " pdb=" OXT ALA C 42 " model vdw 2.393 2.520 nonbonded pdb=" NZ LYS F 28 " pdb=" OXT ALA G 42 " model vdw 2.393 2.520 nonbonded pdb=" OXT ALA E 42 " pdb=" NZ LYS D 28 " model vdw 2.394 2.520 nonbonded pdb=" N ASP E 23 " pdb=" OD1 ASP E 23 " model vdw 2.400 2.520 nonbonded pdb=" N ASP J 23 " pdb=" OD1 ASP J 23 " model vdw 2.400 2.520 ... (remaining 18169 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.380 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 10.960 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.420 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 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 : 0.003 0.014 2290 Z= 0.236 Angle : 0.438 2.812 3080 Z= 0.261 Chirality : 0.057 0.116 370 Planarity : 0.002 0.008 390 Dihedral : 9.968 43.251 770 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 8.70 % Favored : 91.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.75 (0.48), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.56 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS C 13 PHE 0.007 0.002 PHE E 20 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 108 time to evaluate : 0.260 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 108 average time/residue: 0.1261 time to fit residues: 15.9663 Evaluate side-chains 80 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 9.9990 chunk 22 optimal weight: 6.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 0.0670 chunk 15 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 14 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 overall best weight: 1.9724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8740 moved from start: 0.2479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2290 Z= 0.224 Angle : 0.386 2.681 3080 Z= 0.217 Chirality : 0.055 0.134 370 Planarity : 0.002 0.009 390 Dihedral : 4.464 16.791 310 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 3.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 4.35 % Allowed : 21.74 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.76 (0.48), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.57 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS F 14 PHE 0.006 0.001 PHE E 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.233 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 83 average time/residue: 0.0797 time to fit residues: 8.6423 Evaluate side-chains 88 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0265 time to fit residues: 0.6153 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 chunk 7 optimal weight: 7.9990 chunk 27 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 0.0970 chunk 9 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 26 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 14 optimal weight: 6.9990 overall best weight: 4.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: I 14 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8763 moved from start: 0.3008 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.033 2290 Z= 0.442 Angle : 0.490 3.929 3080 Z= 0.262 Chirality : 0.055 0.134 370 Planarity : 0.002 0.007 390 Dihedral : 5.775 31.769 310 Min Nonbonded Distance : 2.274 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 3.48 % Allowed : 19.57 % Favored : 76.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.88 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS G 14 PHE 0.006 0.001 PHE H 20 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 72 time to evaluate : 0.276 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 75 average time/residue: 0.0832 time to fit residues: 8.0156 Evaluate side-chains 77 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 72 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0265 time to fit residues: 0.5860 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 8.9990 chunk 13 optimal weight: 7.9990 chunk 18 optimal weight: 6.9990 chunk 27 optimal weight: 5.9990 chunk 28 optimal weight: 6.9990 chunk 14 optimal weight: 0.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8742 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2290 Z= 0.182 Angle : 0.378 3.370 3080 Z= 0.209 Chirality : 0.055 0.131 370 Planarity : 0.001 0.008 390 Dihedral : 4.995 27.783 310 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 6.96 % Allowed : 15.22 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.83 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS I 14 PHE 0.004 0.001 PHE H 20 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 0.245 Fit side-chains outliers start: 16 outliers final: 5 residues processed: 91 average time/residue: 0.0818 time to fit residues: 9.5570 Evaluate side-chains 84 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 79 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0266 time to fit residues: 0.5490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 10.0000 chunk 11 optimal weight: 7.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 9.9990 chunk 26 optimal weight: 7.9990 chunk 7 optimal weight: 8.9990 chunk 9 optimal weight: 7.9990 chunk 5 optimal weight: 0.8980 chunk 17 optimal weight: 0.8980 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8772 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2290 Z= 0.427 Angle : 0.490 3.670 3080 Z= 0.263 Chirality : 0.054 0.124 370 Planarity : 0.002 0.008 390 Dihedral : 6.002 33.772 310 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.61 % Allowed : 21.74 % Favored : 75.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 14 PHE 0.006 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.254 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 76 average time/residue: 0.0831 time to fit residues: 8.1607 Evaluate side-chains 75 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.278 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0259 time to fit residues: 0.4745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 6.9990 chunk 29 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 13 optimal weight: 7.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 7.9990 chunk 15 optimal weight: 4.9990 chunk 27 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 16 optimal weight: 9.9990 chunk 21 optimal weight: 1.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8766 moved from start: 0.3604 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 2290 Z= 0.367 Angle : 0.464 4.683 3080 Z= 0.251 Chirality : 0.053 0.121 370 Planarity : 0.002 0.008 390 Dihedral : 5.938 33.282 310 Min Nonbonded Distance : 2.298 Molprobity Statistics. All-atom Clashscore : 5.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer: Outliers : 2.17 % Allowed : 22.61 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.02 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS I 14 PHE 0.005 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 74 time to evaluate : 0.257 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 76 average time/residue: 0.0761 time to fit residues: 7.4913 Evaluate side-chains 76 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.200 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0254 time to fit residues: 0.4239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 10.0000 chunk 24 optimal weight: 0.0470 chunk 28 optimal weight: 5.9990 chunk 18 optimal weight: 6.9990 chunk 17 optimal weight: 7.9990 chunk 13 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 8 optimal weight: 6.9990 chunk 5 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 14 optimal weight: 0.8980 overall best weight: 2.1884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8752 moved from start: 0.3653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2290 Z= 0.245 Angle : 0.414 3.320 3080 Z= 0.229 Chirality : 0.054 0.121 370 Planarity : 0.002 0.007 390 Dihedral : 5.508 29.860 310 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.03 % Favored : 98.97 % Rotamer: Outliers : 0.43 % Allowed : 23.48 % Favored : 76.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.96 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 14 PHE 0.004 0.001 PHE H 20 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.272 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 77 average time/residue: 0.0654 time to fit residues: 6.6001 Evaluate side-chains 75 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.195 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 9.9990 chunk 22 optimal weight: 9.9990 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 16 optimal weight: 0.0770 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.8980 overall best weight: 1.1944 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8731 moved from start: 0.3769 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2290 Z= 0.146 Angle : 0.384 4.352 3080 Z= 0.217 Chirality : 0.055 0.123 370 Planarity : 0.002 0.009 390 Dihedral : 4.914 24.659 310 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.38 % Favored : 98.62 % Rotamer: Outliers : 0.87 % Allowed : 25.22 % Favored : 73.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.47), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.90 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 13 PHE 0.003 0.001 PHE E 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 80 time to evaluate : 0.264 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 80 average time/residue: 0.0807 time to fit residues: 8.3791 Evaluate side-chains 77 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0272 time to fit residues: 0.4240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 27 optimal weight: 6.9990 chunk 23 optimal weight: 8.9990 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** J 14 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.3883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.046 2290 Z= 0.647 Angle : 0.638 7.590 3080 Z= 0.339 Chirality : 0.053 0.118 370 Planarity : 0.002 0.012 390 Dihedral : 6.794 37.434 310 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 7.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 0.43 % Allowed : 26.52 % Favored : 73.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS I 14 PHE 0.007 0.001 PHE C 20 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 65 time to evaluate : 0.269 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 66 average time/residue: 0.0831 time to fit residues: 7.1047 Evaluate side-chains 65 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 64 time to evaluate : 0.264 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0251 time to fit residues: 0.3812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 6 optimal weight: 4.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 0.9980 chunk 4 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8729 moved from start: 0.3873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2290 Z= 0.142 Angle : 0.416 5.805 3080 Z= 0.237 Chirality : 0.055 0.124 370 Planarity : 0.002 0.011 390 Dihedral : 5.374 28.328 310 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.43 % Allowed : 25.22 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.97 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 13 PHE 0.004 0.001 PHE C 20 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 580 Ramachandran restraints generated. 290 Oldfield, 0 Emsley, 290 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.270 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.0822 time to fit residues: 8.1068 Evaluate side-chains 77 residues out of total 230 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0282 time to fit residues: 0.4101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 7.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 8.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.099266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.085148 restraints weight = 4855.992| |-----------------------------------------------------------------------------| r_work (start): 0.3124 rms_B_bonded: 3.30 r_work: 0.2974 rms_B_bonded: 3.69 restraints_weight: 0.5000 r_work (final): 0.2974 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2290 Z= 0.230 Angle : 0.466 6.468 3080 Z= 0.259 Chirality : 0.054 0.122 370 Planarity : 0.002 0.009 390 Dihedral : 5.516 28.059 310 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 0.00 % Allowed : 25.65 % Favored : 74.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.46), residues: 290 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.35), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.000 HIS I 14 PHE 0.005 0.001 PHE C 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 917.99 seconds wall clock time: 17 minutes 12.58 seconds (1032.58 seconds total)