Starting phenix.real_space_refine on Sun Mar 10 15:01:41 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/03_2024/7ynr_33969_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/03_2024/7ynr_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_33969/03_2024/7ynr_33969.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/03_2024/7ynr_33969.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/03_2024/7ynr_33969_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynr_33969/03_2024/7ynr_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-dev-5265/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: 1.76, per 1000 atoms: 0.70 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: 0.81 Conformation dependent library (CDL) restraints added in 504.4 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: 0.35 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: 0.60 Time building geometry restraints manager: 0.91 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: 1.890 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: 9.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 11.730 Find NCS groups from input model: 0.160 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:12.600 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.590 ------------------------------------------------------------------------------- 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 : 0.265 Fit side-chains REVERT: F 43 LYS cc_start: 0.8683 (mttt) cc_final: 0.8468 (mttp) outliers start: 0 outliers final: 0 residues processed: 13 average time/residue: 2.1290 time to fit residues: 28.3681 Evaluate side-chains 11 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.265 ------------------------------------------------------------------------------- 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: 4.9990 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: 0.0836 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 3.993 3432 Z= 0.267 Chirality : 0.051 0.121 456 Planarity : 0.002 0.008 420 Dihedral : 4.253 12.116 366 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.50 % Favored : 93.50 % 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: -2.84 (0.40), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.16 (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 : 0.278 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 10 average time/residue: 2.1563 time to fit residues: 22.2191 Evaluate side-chains 5 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 5 time to evaluate : 0.275 ------------------------------------------------------------------------------- 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: 2.9990 chunk 27 optimal weight: 2.9990 chunk 22 optimal weight: 0.0570 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 5.9990 chunk 35 optimal weight: 0.4980 chunk 29 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 10.0000 overall best weight: 1.0300 ------------------------------------------------------------------------------- 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: 0.8229 moved from start: 0.1122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.010 2538 Z= 0.151 Angle : 0.399 3.732 3432 Z= 0.230 Chirality : 0.051 0.121 456 Planarity : 0.001 0.006 420 Dihedral : 3.858 10.967 366 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.82 % Favored : 97.18 % Rotamer: Outliers : 1.16 % Allowed : 6.59 % 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: -2.40 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.82 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.009 0.002 PHE C 94 TYR 0.003 0.001 TYR F 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 14 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 11 time to evaluate : 0.272 Fit side-chains outliers start: 3 outliers final: 0 residues processed: 14 average time/residue: 1.7115 time to fit residues: 24.6784 Evaluate side-chains 8 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.279 ------------------------------------------------------------------------------- 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: 5.9990 chunk 15 optimal weight: 2.9990 chunk 21 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 5.9990 chunk 31 optimal weight: 7.9990 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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: 0.8271 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.024 2538 Z= 0.352 Angle : 0.494 4.722 3432 Z= 0.285 Chirality : 0.052 0.123 456 Planarity : 0.002 0.008 420 Dihedral : 4.244 12.537 366 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 5.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Rotamer: Outliers : 1.55 % Allowed : 6.20 % 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: -2.30 (0.43), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.74 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS C 50 PHE 0.012 0.003 PHE F 94 TYR 0.008 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 12 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 8 time to evaluate : 0.253 Fit side-chains outliers start: 4 outliers final: 0 residues processed: 11 average time/residue: 1.5456 time to fit residues: 17.6323 Evaluate side-chains 7 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.250 ------------------------------------------------------------------------------- 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: 1.9990 chunk 14 optimal weight: 8.9990 chunk 29 optimal weight: 0.6980 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 8 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 overall best weight: 1.8986 ------------------------------------------------------------------------------- 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: 0.8260 moved from start: 0.1237 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= 0.260 Angle : 0.472 4.555 3432 Z= 0.272 Chirality : 0.052 0.122 456 Planarity : 0.002 0.007 420 Dihedral : 4.201 12.222 366 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: -2.13 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.61 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.011 0.003 PHE C 94 TYR 0.006 0.001 TYR F 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 : 0.294 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 2.2169 time to fit residues: 18.3306 Evaluate side-chains 8 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.285 ------------------------------------------------------------------------------- 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: 6.9990 chunk 28 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 1.9990 overall best weight: 2.1786 ------------------------------------------------------------------------------- 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: 0.8266 moved from start: 0.1275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2538 Z= 0.295 Angle : 0.470 4.677 3432 Z= 0.270 Chirality : 0.052 0.122 456 Planarity : 0.002 0.008 420 Dihedral : 4.207 12.484 366 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer: Outliers : 0.00 % Allowed : 7.75 % 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: -2.10 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.33), 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 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 7 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 2.3072 time to fit residues: 16.7477 Evaluate side-chains 7 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.291 ------------------------------------------------------------------------------- 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: 1.9990 chunk 29 optimal weight: 0.0570 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 overall best weight: 2.0106 ------------------------------------------------------------------------------- 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: 0.1311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.018 2538 Z= 0.272 Angle : 0.456 4.599 3432 Z= 0.263 Chirality : 0.051 0.122 456 Planarity : 0.002 0.008 420 Dihedral : 4.190 12.377 366 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % 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: -2.04 (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 0.005 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: 0 poor density : 8 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 2.3560 time to fit residues: 19.4602 Evaluate side-chains 8 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.273 ------------------------------------------------------------------------------- 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: 2.9990 chunk 3 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 33 optimal weight: 0.8980 chunk 30 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 4.9990 chunk 14 optimal weight: 6.9990 chunk 25 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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: 0.8252 moved from start: 0.1367 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= 0.211 Angle : 0.429 4.379 3432 Z= 0.247 Chirality : 0.051 0.123 456 Planarity : 0.002 0.007 420 Dihedral : 3.993 11.978 366 Min Nonbonded Distance : 2.413 Molprobity Statistics. All-atom Clashscore : 4.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.08 % Favored : 94.92 % 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: -1.98 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.50 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.010 0.002 PHE C 94 TYR 0.004 0.001 TYR C 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: 0 poor density : 8 time to evaluate : 0.366 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 2.3486 time to fit residues: 19.4061 Evaluate side-chains 7 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.334 ------------------------------------------------------------------------------- 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: 0.5980 chunk 30 optimal weight: 8.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 0.0370 chunk 34 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 overall best weight: 0.7058 ------------------------------------------------------------------------------- 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: 0.8214 moved from start: 0.1583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.012 2538 Z= 0.110 Angle : 0.390 3.851 3432 Z= 0.226 Chirality : 0.051 0.124 456 Planarity : 0.001 0.005 420 Dihedral : 3.644 10.870 366 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 3.26 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: -1.85 (0.45), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.35), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.007 0.002 PHE C 94 TYR 0.003 0.000 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 7 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 7 time to evaluate : 0.274 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 7 average time/residue: 2.2036 time to fit residues: 16.0190 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 ------------------------------------------------------------------------------- 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: 0.9980 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 8.9990 chunk 8 optimal weight: 4.9990 chunk 26 optimal weight: 0.7980 chunk 4 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- 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: 0.8271 moved from start: 0.1370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.023 2538 Z= 0.340 Angle : 0.476 4.767 3432 Z= 0.274 Chirality : 0.051 0.120 456 Planarity : 0.002 0.009 420 Dihedral : 4.217 12.727 366 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % 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: -1.97 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.49 (0.34), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.004 HIS C 50 PHE 0.012 0.003 PHE F 94 TYR 0.007 0.002 TYR F 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 : 0.284 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 2.1501 time to fit residues: 13.4690 Evaluate side-chains 6 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.271 ------------------------------------------------------------------------------- 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: 2.9990 chunk 5 optimal weight: 7.9990 chunk 25 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 20 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 19 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 0 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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 = 0.3983 r_free = 0.3983 target = 0.131489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.103592 restraints weight = 2861.986| |-----------------------------------------------------------------------------| r_work (start): 0.3737 rms_B_bonded: 2.11 r_work: 0.3645 rms_B_bonded: 2.27 restraints_weight: 0.5000 r_work: 0.3533 rms_B_bonded: 3.69 restraints_weight: 0.2500 r_work (final): 0.3533 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.1402 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= 0.243 Angle : 0.440 4.522 3432 Z= 0.254 Chirality : 0.051 0.122 456 Planarity : 0.002 0.007 420 Dihedral : 4.079 12.218 366 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.24 % Favored : 95.76 % 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: -1.94 (0.44), residues: 354 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.47 (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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1233.10 seconds wall clock time: 22 minutes 39.41 seconds (1359.41 seconds total)