Starting phenix.real_space_refine on Thu Dec 7 16:33:14 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/12_2023/7ynr_33969_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/12_2023/7ynr_33969.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/12_2023/7ynr_33969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/12_2023/7ynr_33969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/12_2023/7ynr_33969_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/12_2023/7ynr_33969_neut.pdb" } resolution = 2.9 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: 3 Type Number sf(0) Gaussians C 1590 2.51 5 N 438 2.21 5 O 498 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: 2526 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "B" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "C" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "D" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "E" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Chain: "F" Number of atoms: 421 Number of conformers: 1 Conformer: "" Number of residues, atoms: 61, 421 Classifications: {'peptide': 61} Link IDs: {'TRANS': 60} Time building chain proxies: 1.67, per 1000 atoms: 0.66 Number of scatterers: 2526 At special positions: 0 Unit cell: (101.352, 104.648, 31.312, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 498 8.00 N 438 7.00 C 1590 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: 0.89 Conformation dependent library (CDL) restraints added in 480.0 milliseconds 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 59.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 38 through 39 removed outlier: 6.851A pdb=" N LEU B 38 " --> pdb=" O TYR C 39 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 45 through 58 removed outlier: 6.917A pdb=" N GLU C 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLY A 47 " --> pdb=" O GLU C 46 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N VAL C 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.931A pdb=" N ALA A 53 " --> pdb=" O VAL C 52 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR C 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N VAL A 55 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N ALA C 56 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N GLU A 57 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 6.837A pdb=" N LYS C 58 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 5.467A pdb=" N GLU B 46 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 8.907A pdb=" N VAL C 49 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.212A pdb=" N VAL B 48 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 8.275A pdb=" N GLY C 51 " --> pdb=" O VAL B 48 " (cutoff:3.500A) removed outlier: 8.631A pdb=" N HIS B 50 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 8.296A pdb=" N ALA C 53 " --> pdb=" O HIS B 50 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N VAL B 52 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 10.441A pdb=" N VAL C 55 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N THR B 54 " --> pdb=" O VAL C 55 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N GLU C 57 " --> pdb=" O THR B 54 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ALA B 56 " --> pdb=" O GLU C 57 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 61 through 66 removed outlier: 6.567A pdb=" N GLN B 62 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 8.212A pdb=" N ASN C 65 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 6.347A pdb=" N THR B 64 " --> pdb=" O ASN C 65 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 69 through 82 removed outlier: 6.325A pdb=" N VAL A 70 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 8.115A pdb=" N GLY C 73 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 8.703A pdb=" N THR A 72 " --> pdb=" O GLY C 73 " (cutoff:3.500A) removed outlier: 7.873A pdb=" N THR C 75 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 9.076A pdb=" N VAL A 74 " --> pdb=" O THR C 75 " (cutoff:3.500A) removed outlier: 9.284A pdb=" N VAL C 77 " --> pdb=" O VAL A 74 " (cutoff:3.500A) removed outlier: 6.858A pdb=" N ALA A 76 " --> pdb=" O VAL C 77 " (cutoff:3.500A) removed outlier: 8.591A pdb=" N GLN C 79 " --> pdb=" O ALA A 76 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA A 78 " --> pdb=" O GLN C 79 " (cutoff:3.500A) removed outlier: 8.549A pdb=" N THR C 81 " --> pdb=" O ALA A 78 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N LYS A 80 " --> pdb=" O THR C 81 " (cutoff:3.500A) removed outlier: 6.792A pdb=" N VAL C 74 " --> pdb=" O GLY B 73 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N THR B 75 " --> pdb=" O VAL C 74 " (cutoff:3.500A) removed outlier: 6.846A pdb=" N ALA C 76 " --> pdb=" O THR B 75 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 89 through 92 removed outlier: 6.309A pdb=" N ALA A 90 " --> pdb=" O ALA C 91 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 95 through 96 removed outlier: 6.176A pdb=" N VAL A 95 " --> pdb=" O LYS C 96 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 38 through 39 removed outlier: 6.851A pdb=" N LEU E 38 " --> pdb=" O TYR F 39 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 45 through 58 removed outlier: 6.931A pdb=" N GLU F 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLY D 47 " --> pdb=" O GLU F 46 " (cutoff:3.500A) removed outlier: 6.911A pdb=" N VAL F 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.934A pdb=" N ALA D 53 " --> pdb=" O VAL F 52 " (cutoff:3.500A) removed outlier: 6.908A pdb=" N THR F 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N VAL D 55 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 6.930A pdb=" N ALA F 56 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N GLU D 57 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.831A pdb=" N LYS F 58 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 5.464A pdb=" N GLU E 46 " --> pdb=" O GLY F 47 " (cutoff:3.500A) removed outlier: 8.909A pdb=" N VAL F 49 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.216A pdb=" N VAL E 48 " --> pdb=" O VAL F 49 " (cutoff:3.500A) removed outlier: 8.282A pdb=" N GLY F 51 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 8.632A pdb=" N HIS E 50 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 8.294A pdb=" N ALA F 53 " --> pdb=" O HIS E 50 " (cutoff:3.500A) removed outlier: 9.055A pdb=" N VAL E 52 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 10.439A pdb=" N VAL F 55 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 8.991A pdb=" N THR E 54 " --> pdb=" O VAL F 55 " (cutoff:3.500A) removed outlier: 10.158A pdb=" N GLU F 57 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 9.050A pdb=" N ALA E 56 " --> pdb=" O GLU F 57 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 61 through 66 removed outlier: 6.566A pdb=" N GLN E 62 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 8.207A pdb=" N ASN F 65 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N THR E 64 " --> pdb=" O ASN F 65 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 69 through 82 removed outlier: 6.337A pdb=" N VAL D 70 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 8.127A pdb=" N GLY F 73 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 8.714A pdb=" N THR D 72 " --> pdb=" O GLY F 73 " (cutoff:3.500A) removed outlier: 7.881A pdb=" N THR F 75 " --> pdb=" O THR D 72 " (cutoff:3.500A) removed outlier: 9.086A pdb=" N VAL D 74 " --> pdb=" O THR F 75 " (cutoff:3.500A) removed outlier: 9.292A pdb=" N VAL F 77 " --> pdb=" O VAL D 74 " (cutoff:3.500A) removed outlier: 6.860A pdb=" N ALA D 76 " --> pdb=" O VAL F 77 " (cutoff:3.500A) removed outlier: 8.589A pdb=" N GLN F 79 " --> pdb=" O ALA D 76 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ALA D 78 " --> pdb=" O GLN F 79 " (cutoff:3.500A) removed outlier: 8.547A pdb=" N THR F 81 " --> pdb=" O ALA D 78 " (cutoff:3.500A) removed outlier: 6.385A pdb=" N LYS D 80 " --> pdb=" O THR F 81 " (cutoff:3.500A) removed outlier: 6.798A pdb=" N VAL F 74 " --> pdb=" O GLY E 73 " (cutoff:3.500A) removed outlier: 6.895A pdb=" N THR E 75 " --> pdb=" O VAL F 74 " (cutoff:3.500A) removed outlier: 6.850A pdb=" N ALA F 76 " --> pdb=" O THR E 75 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 89 through 92 removed outlier: 6.305A pdb=" N ALA D 90 " --> pdb=" O ALA F 91 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'D' and resid 95 through 96 removed outlier: 6.175A pdb=" N VAL D 95 " --> pdb=" O LYS F 96 " (cutoff:3.500A) 48 hydrogen bonds defined for protein. 144 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.57 Time building geometry restraints manager: 0.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 432 1.29 - 1.35: 396 1.35 - 1.42: 102 1.42 - 1.48: 414 1.48 - 1.54: 1194 Bond restraints: 2538 Sorted by residual: bond pdb=" CG LEU B 38 " pdb=" CD1 LEU B 38 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.11e-01 bond pdb=" CG LEU A 38 " pdb=" CD1 LEU A 38 " ideal model delta sigma weight residual 1.521 1.500 0.021 3.30e-02 9.18e+02 4.00e-01 bond pdb=" CG LEU E 38 " pdb=" CD1 LEU E 38 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.79e-01 bond pdb=" CG LEU D 38 " pdb=" CD1 LEU D 38 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.76e-01 bond pdb=" CG LEU F 38 " pdb=" CD1 LEU F 38 " ideal model delta sigma weight residual 1.521 1.501 0.020 3.30e-02 9.18e+02 3.72e-01 ... (remaining 2533 not shown) Histogram of bond angle deviations from ideal: 106.07 - 111.11: 1153 111.11 - 116.14: 653 116.14 - 121.18: 841 121.18 - 126.21: 779 126.21 - 131.25: 6 Bond angle restraints: 3432 Sorted by residual: angle pdb=" N GLY B 73 " pdb=" CA GLY B 73 " pdb=" C GLY B 73 " ideal model delta sigma weight residual 113.18 116.24 -3.06 2.37e+00 1.78e-01 1.67e+00 angle pdb=" N GLY C 73 " pdb=" CA GLY C 73 " pdb=" C GLY C 73 " ideal model delta sigma weight residual 113.18 116.23 -3.05 2.37e+00 1.78e-01 1.66e+00 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 121.85 119.58 2.27 1.77e+00 3.19e-01 1.65e+00 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 121.85 119.58 2.27 1.77e+00 3.19e-01 1.64e+00 angle pdb=" N GLY E 73 " pdb=" CA GLY E 73 " pdb=" C GLY E 73 " ideal model delta sigma weight residual 113.18 116.20 -3.02 2.37e+00 1.78e-01 1.62e+00 ... (remaining 3427 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.79: 1272 8.79 - 17.59: 132 17.59 - 26.38: 48 26.38 - 35.18: 12 35.18 - 43.97: 18 Dihedral angle restraints: 1482 sinusoidal: 492 harmonic: 990 Sorted by residual: dihedral pdb=" CA THR D 72 " pdb=" C THR D 72 " pdb=" N GLY D 73 " pdb=" CA GLY D 73 " ideal model delta harmonic sigma weight residual 180.00 169.18 10.82 0 5.00e+00 4.00e-02 4.68e+00 dihedral pdb=" CA THR F 72 " pdb=" C THR F 72 " pdb=" N GLY F 73 " pdb=" CA GLY F 73 " ideal model delta harmonic sigma weight residual 180.00 169.19 10.81 0 5.00e+00 4.00e-02 4.67e+00 dihedral pdb=" CA THR A 72 " pdb=" C THR A 72 " pdb=" N GLY A 73 " pdb=" CA GLY A 73 " ideal model delta harmonic sigma weight residual 180.00 169.20 10.80 0 5.00e+00 4.00e-02 4.67e+00 ... (remaining 1479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 255 0.025 - 0.050: 70 0.050 - 0.075: 53 0.075 - 0.100: 24 0.100 - 0.125: 54 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA VAL E 49 " pdb=" N VAL E 49 " pdb=" C VAL E 49 " pdb=" CB VAL E 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA VAL C 49 " pdb=" N VAL C 49 " pdb=" C VAL C 49 " pdb=" CB VAL C 49 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.87e-01 chirality pdb=" CA VAL F 49 " pdb=" N VAL F 49 " pdb=" C VAL F 49 " pdb=" CB VAL F 49 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.78e-01 ... (remaining 453 not shown) Planarity restraints: 420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS A 50 " -0.007 2.00e-02 2.50e+03 5.91e-03 5.24e-01 pdb=" CG HIS A 50 " 0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS A 50 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS A 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS A 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS A 50 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS D 50 " 0.007 2.00e-02 2.50e+03 5.89e-03 5.20e-01 pdb=" CG HIS D 50 " -0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS D 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS D 50 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS D 50 " 0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS D 50 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB HIS C 50 " -0.007 2.00e-02 2.50e+03 5.87e-03 5.16e-01 pdb=" CG HIS C 50 " 0.012 2.00e-02 2.50e+03 pdb=" ND1 HIS C 50 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 HIS C 50 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 HIS C 50 " -0.002 2.00e-02 2.50e+03 pdb=" NE2 HIS C 50 " -0.002 2.00e-02 2.50e+03 ... (remaining 417 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1003 2.92 - 3.41: 2104 3.41 - 3.91: 3991 3.91 - 4.40: 4105 4.40 - 4.90: 8617 Nonbonded interactions: 19820 Sorted by model distance: nonbonded pdb=" NZ LYS F 60 " pdb=" OE1 GLN F 62 " model vdw 2.424 2.520 nonbonded pdb=" NZ LYS A 60 " pdb=" OE1 GLN A 62 " model vdw 2.425 2.520 nonbonded pdb=" NZ LYS D 60 " pdb=" OE1 GLN D 62 " model vdw 2.425 2.520 nonbonded pdb=" NZ LYS B 60 " pdb=" OE1 GLN B 62 " model vdw 2.425 2.520 nonbonded pdb=" NZ LYS C 60 " pdb=" OE1 GLN C 62 " model vdw 2.425 2.520 ... (remaining 19815 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' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.010 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: 9.170 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.830 Find NCS groups from input model: 0.180 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:12.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 0.021 2538 Z= 0.216 Angle : 0.459 3.058 3432 Z= 0.261 Chirality : 0.052 0.125 456 Planarity : 0.002 0.006 420 Dihedral : 10.047 43.973 858 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.69 % Favored : 98.31 % Rotamer: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: -3.30 (0.38), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.51 (0.29), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS D 50 PHE 0.009 0.002 PHE A 94 TYR 0.005 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 13 time to evaluate : 0.297 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 2.1670 time to fit residues: 28.9151 Evaluate side-chains 11 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 30 optimal weight: 9.9990 chunk 27 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 chunk 14 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 17 optimal weight: 9.9990 chunk 21 optimal weight: 0.6980 chunk 32 optimal weight: 7.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- 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: 0.8262 moved from start: 0.0845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2538 Z= 0.294 Angle : 0.462 3.992 3432 Z= 0.266 Chirality : 0.051 0.120 456 Planarity : 0.002 0.007 420 Dihedral : 4.253 12.127 366 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.21 % Favored : 93.79 % Rotamer: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.83 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.15 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.012 0.003 PHE F 94 TYR 0.007 0.002 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.252 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 2.2293 time to fit residues: 22.8997 Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3676 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 18 optimal weight: 10.0000 chunk 10 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 26 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 overall best weight: 1.5188 ------------------------------------------------------------------------------- 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: 0.8247 moved from start: 0.1063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.014 2538 Z= 0.210 Angle : 0.422 3.977 3432 Z= 0.243 Chirality : 0.051 0.122 456 Planarity : 0.001 0.007 420 Dihedral : 4.045 11.679 366 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.78 % Allowed : 6.98 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.44 (0.42), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.85 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.010 0.002 PHE F 94 TYR 0.004 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 8 time to evaluate : 0.268 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 10 average time/residue: 1.7606 time to fit residues: 18.2339 Evaluate side-chains 6 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 4.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 6.9990 chunk 9 optimal weight: 3.9990 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- 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: 0.8264 moved from start: 0.1145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 2538 Z= 0.299 Angle : 0.471 4.593 3432 Z= 0.271 Chirality : 0.051 0.122 456 Planarity : 0.002 0.008 420 Dihedral : 4.170 12.494 366 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 2.33 % Allowed : 5.43 % Favored : 92.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.73 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.012 0.003 PHE F 94 TYR 0.006 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 7 time to evaluate : 0.285 Fit side-chains outliers start: 6 outliers final: 0 residues processed: 11 average time/residue: 1.3808 time to fit residues: 15.8691 Evaluate side-chains 7 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 0 optimal weight: 10.0000 chunk 25 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 9.9990 chunk 31 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- 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: 0.8284 moved from start: 0.1200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.028 2538 Z= 0.422 Angle : 0.543 4.984 3432 Z= 0.312 Chirality : 0.053 0.122 456 Planarity : 0.002 0.009 420 Dihedral : 4.567 13.181 366 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 5.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.19 % Favored : 91.81 % Rotamer: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % 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: -2.23 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.69 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS C 50 PHE 0.014 0.004 PHE F 94 TYR 0.008 0.002 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.265 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 2.1280 time to fit residues: 17.6303 Evaluate side-chains 8 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.281 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 8 optimal weight: 3.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 16 optimal weight: 3.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 19 optimal weight: 0.3980 chunk 25 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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: 0.8241 moved from start: 0.1320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.017 2538 Z= 0.175 Angle : 0.435 4.278 3432 Z= 0.250 Chirality : 0.051 0.123 456 Planarity : 0.001 0.007 420 Dihedral : 3.980 11.660 366 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.00 % Allowed : 8.53 % Favored : 91.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.02 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.53 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.009 0.002 PHE F 94 TYR 0.004 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 10 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 2.2743 time to fit residues: 23.4020 Evaluate side-chains 8 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.255 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 21 optimal weight: 6.9990 chunk 16 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 8.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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: 0.8263 moved from start: 0.1310 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.019 2538 Z= 0.291 Angle : 0.466 4.649 3432 Z= 0.268 Chirality : 0.051 0.122 456 Planarity : 0.002 0.008 420 Dihedral : 4.188 12.416 366 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.39 % Allowed : 8.91 % Favored : 90.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.54 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.011 0.003 PHE F 94 TYR 0.006 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.274 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 7 average time/residue: 2.2326 time to fit residues: 16.2261 Evaluate side-chains 7 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.274 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 17 optimal weight: 0.0170 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 chunk 14 optimal weight: 5.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 4.9990 overall best weight: 1.1824 ------------------------------------------------------------------------------- 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: 0.8237 moved from start: 0.1424 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 2538 Z= 0.170 Angle : 0.416 4.205 3432 Z= 0.240 Chirality : 0.051 0.123 456 Planarity : 0.001 0.006 420 Dihedral : 3.873 11.500 366 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.39 % Allowed : 8.91 % Favored : 90.70 % 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: -1.95 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.009 0.002 PHE F 94 TYR 0.003 0.001 TYR F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 7 time to evaluate : 0.300 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 7 average time/residue: 2.2731 time to fit residues: 16.5004 Evaluate side-chains 7 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 6 time to evaluate : 0.296 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.4800 time to fit residues: 1.8823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 29 optimal weight: 8.9990 chunk 30 optimal weight: 10.0000 chunk 32 optimal weight: 6.9990 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 2.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- 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: 0.8254 moved from start: 0.1387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.016 2538 Z= 0.246 Angle : 0.441 4.485 3432 Z= 0.254 Chirality : 0.051 0.122 456 Planarity : 0.002 0.007 420 Dihedral : 4.028 12.113 366 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % Rotamer: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % 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: -1.95 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.010 0.003 PHE F 94 TYR 0.005 0.001 TYR C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.264 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 5 average time/residue: 2.2475 time to fit residues: 11.7795 Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 2 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 30 optimal weight: 10.0000 chunk 8 optimal weight: 0.0770 chunk 26 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 28 optimal weight: 0.7980 chunk 11 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 overall best weight: 0.9540 ------------------------------------------------------------------------------- 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: 0.8226 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 2538 Z= 0.138 Angle : 0.403 4.064 3432 Z= 0.233 Chirality : 0.051 0.123 456 Planarity : 0.001 0.006 420 Dihedral : 3.748 11.244 366 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % 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: -1.86 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.41 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.008 0.002 PHE F 94 TYR 0.003 0.001 TYR C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 708 Ramachandran restraints generated. 354 Oldfield, 0 Emsley, 354 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.277 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 2.2403 time to fit residues: 14.0166 Evaluate side-chains 6 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 3 optimal weight: 5.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.129715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3614 r_free = 0.3614 target = 0.101937 restraints weight = 2880.426| |-----------------------------------------------------------------------------| r_work (start): 0.3653 rms_B_bonded: 2.08 r_work: 0.3555 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3442 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3442 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.031 2538 Z= 0.447 Angle : 0.523 5.063 3432 Z= 0.300 Chirality : 0.053 0.121 456 Planarity : 0.002 0.009 420 Dihedral : 4.445 13.168 366 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.47 % Favored : 91.53 % Rotamer: Outliers : 0.00 % Allowed : 10.08 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.06 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.56 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.004 HIS C 50 PHE 0.014 0.004 PHE F 94 TYR 0.008 0.002 TYR F 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1154.33 seconds wall clock time: 21 minutes 23.09 seconds (1283.09 seconds total)