Starting phenix.real_space_refine on Thu Dec 7 16:15:04 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynt_33971/12_2023/7ynt_33971.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynt_33971/12_2023/7ynt_33971.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynt_33971/12_2023/7ynt_33971.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynt_33971/12_2023/7ynt_33971.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynt_33971/12_2023/7ynt_33971.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ynt_33971/12_2023/7ynt_33971.pdb" } resolution = 3.1 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= 0.001 sd= 0.004 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 1470 2.51 5 N 420 2.21 5 O 474 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: 2364 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "A" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "B" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "C" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "D" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Chain: "E" Number of atoms: 394 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 394 Classifications: {'peptide': 58} Link IDs: {'TRANS': 57} Time building chain proxies: 1.56, per 1000 atoms: 0.66 Number of scatterers: 2364 At special positions: 0 Unit cell: (85.86, 107.06, 32.86, 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 474 8.00 N 420 7.00 C 1470 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.76 Conformation dependent library (CDL) restraints added in 415.8 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 588 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 12 sheets defined 0.0% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'F' and resid 44 through 55 removed outlier: 6.928A pdb=" N LYS F 45 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N GLU A 46 " --> pdb=" O LYS F 45 " (cutoff:3.500A) removed outlier: 6.907A pdb=" N GLY F 47 " --> pdb=" O GLU A 46 " (cutoff:3.500A) removed outlier: 6.964A pdb=" N VAL A 52 " --> pdb=" O GLY F 51 " (cutoff:3.500A) removed outlier: 6.922A pdb=" N ALA F 53 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N THR A 54 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N VAL F 55 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 6.973A pdb=" N LYS A 45 " --> pdb=" O THR B 44 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N GLU B 46 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 6.953A pdb=" N GLY A 47 " --> pdb=" O GLU B 46 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL B 52 " --> pdb=" O GLY A 51 " (cutoff:3.500A) removed outlier: 6.896A pdb=" N ALA A 53 " --> pdb=" O VAL B 52 " (cutoff:3.500A) removed outlier: 6.833A pdb=" N THR B 54 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N VAL A 55 " --> pdb=" O THR B 54 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'F' and resid 58 through 66 removed outlier: 6.084A pdb=" N THR F 59 " --> pdb=" O LYS A 60 " (cutoff:3.500A) removed outlier: 7.908A pdb=" N GLN A 62 " --> pdb=" O THR F 59 " (cutoff:3.500A) removed outlier: 6.346A pdb=" N GLU F 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 7.821A pdb=" N THR A 64 " --> pdb=" O GLU F 61 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL F 63 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.638A pdb=" N VAL A 66 " --> pdb=" O VAL F 63 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N ASN F 65 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.060A pdb=" N THR A 59 " --> pdb=" O LYS B 60 " (cutoff:3.500A) removed outlier: 7.897A pdb=" N GLN B 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.815A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.736A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.642A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 7.015A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'F' and resid 69 through 75 removed outlier: 6.857A pdb=" N VAL A 70 " --> pdb=" O ALA F 69 " (cutoff:3.500A) removed outlier: 6.943A pdb=" N VAL F 71 " --> pdb=" O VAL A 70 " (cutoff:3.500A) removed outlier: 6.965A pdb=" N THR A 72 " --> pdb=" O VAL F 71 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N VAL B 70 " --> pdb=" O ALA A 69 " (cutoff:3.500A) removed outlier: 6.967A pdb=" N VAL A 71 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 6.977A pdb=" N THR B 72 " --> pdb=" O VAL A 71 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'F' and resid 78 through 79 removed outlier: 6.708A pdb=" N ALA F 78 " --> pdb=" O GLN A 79 " (cutoff:3.500A) removed outlier: 6.726A pdb=" N ALA A 78 " --> pdb=" O GLN B 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'F' and resid 94 through 95 removed outlier: 5.979A pdb=" N PHE F 94 " --> pdb=" O VAL A 95 " (cutoff:3.500A) removed outlier: 5.995A pdb=" N PHE A 94 " --> pdb=" O VAL B 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 87 through 89 removed outlier: 5.723A pdb=" N ILE A 88 " --> pdb=" O ALA B 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'C' and resid 44 through 55 removed outlier: 6.953A pdb=" N LYS C 45 " --> pdb=" O THR D 44 " (cutoff:3.500A) removed outlier: 6.942A pdb=" N GLU D 46 " --> pdb=" O LYS C 45 " (cutoff:3.500A) removed outlier: 6.927A pdb=" N GLY C 47 " --> pdb=" O GLU D 46 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N VAL D 52 " --> pdb=" O GLY C 51 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N ALA C 53 " --> pdb=" O VAL D 52 " (cutoff:3.500A) removed outlier: 6.854A pdb=" N THR D 54 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.918A pdb=" N VAL C 55 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 6.958A pdb=" N LYS D 45 " --> pdb=" O THR E 44 " (cutoff:3.500A) removed outlier: 6.948A pdb=" N GLU E 46 " --> pdb=" O LYS D 45 " (cutoff:3.500A) removed outlier: 6.946A pdb=" N GLY D 47 " --> pdb=" O GLU E 46 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N VAL E 52 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N ALA D 53 " --> pdb=" O VAL E 52 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N THR E 54 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.880A pdb=" N VAL D 55 " --> pdb=" O THR E 54 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'C' and resid 58 through 66 removed outlier: 6.068A pdb=" N THR C 59 " --> pdb=" O LYS D 60 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N GLN D 62 " --> pdb=" O THR C 59 " (cutoff:3.500A) removed outlier: 6.339A pdb=" N GLU C 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.814A pdb=" N THR D 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.730A pdb=" N VAL C 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.635A pdb=" N VAL D 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N ASN C 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.073A pdb=" N THR D 59 " --> pdb=" O LYS E 60 " (cutoff:3.500A) removed outlier: 7.912A pdb=" N GLN E 62 " --> pdb=" O THR D 59 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.755A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.662A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 7.040A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'C' and resid 69 through 75 removed outlier: 6.855A pdb=" N VAL D 70 " --> pdb=" O ALA C 69 " (cutoff:3.500A) removed outlier: 6.939A pdb=" N VAL C 71 " --> pdb=" O VAL D 70 " (cutoff:3.500A) removed outlier: 6.959A pdb=" N THR D 72 " --> pdb=" O VAL C 71 " (cutoff:3.500A) removed outlier: 6.913A pdb=" N VAL E 70 " --> pdb=" O ALA D 69 " (cutoff:3.500A) removed outlier: 6.985A pdb=" N VAL D 71 " --> pdb=" O VAL E 70 " (cutoff:3.500A) removed outlier: 6.989A pdb=" N THR E 72 " --> pdb=" O VAL D 71 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 78 through 79 removed outlier: 6.720A pdb=" N ALA C 78 " --> pdb=" O GLN D 79 " (cutoff:3.500A) removed outlier: 6.727A pdb=" N ALA D 78 " --> pdb=" O GLN E 79 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'C' and resid 87 through 89 removed outlier: 5.718A pdb=" N ILE C 88 " --> pdb=" O ALA D 89 " (cutoff:3.500A) removed outlier: 5.721A pdb=" N ILE D 88 " --> pdb=" O ALA E 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 94 through 95 removed outlier: 5.981A pdb=" N PHE C 94 " --> pdb=" O VAL D 95 " (cutoff:3.500A) removed outlier: 6.006A pdb=" N PHE D 94 " --> pdb=" O VAL E 95 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB3 28 hydrogen bonds defined for protein. 84 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: 0.50 Time building geometry restraints manager: 0.85 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: 414 1.29 - 1.35: 378 1.35 - 1.42: 60 1.42 - 1.48: 396 1.48 - 1.54: 1122 Bond restraints: 2370 Sorted by residual: bond pdb=" C THR D 92 " pdb=" N GLY D 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 2.18e+00 bond pdb=" C THR A 92 " pdb=" N GLY A 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 2.16e+00 bond pdb=" C THR E 92 " pdb=" N GLY E 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 1.97e+00 bond pdb=" C THR C 92 " pdb=" N GLY C 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 1.88e+00 bond pdb=" C THR B 92 " pdb=" N GLY B 93 " ideal model delta sigma weight residual 1.332 1.325 0.007 5.00e-03 4.00e+04 1.85e+00 ... (remaining 2365 not shown) Histogram of bond angle deviations from ideal: 103.06 - 108.72: 168 108.72 - 114.38: 1440 114.38 - 120.03: 474 120.03 - 125.69: 1110 125.69 - 131.35: 6 Bond angle restraints: 3198 Sorted by residual: angle pdb=" N PHE A 94 " pdb=" CA PHE A 94 " pdb=" C PHE A 94 " ideal model delta sigma weight residual 108.24 103.06 5.18 1.81e+00 3.05e-01 8.19e+00 angle pdb=" N PHE E 94 " pdb=" CA PHE E 94 " pdb=" C PHE E 94 " ideal model delta sigma weight residual 108.24 103.08 5.16 1.81e+00 3.05e-01 8.12e+00 angle pdb=" N PHE B 94 " pdb=" CA PHE B 94 " pdb=" C PHE B 94 " ideal model delta sigma weight residual 108.24 103.08 5.16 1.81e+00 3.05e-01 8.12e+00 angle pdb=" N PHE D 94 " pdb=" CA PHE D 94 " pdb=" C PHE D 94 " ideal model delta sigma weight residual 108.24 103.09 5.15 1.81e+00 3.05e-01 8.09e+00 angle pdb=" N PHE F 94 " pdb=" CA PHE F 94 " pdb=" C PHE F 94 " ideal model delta sigma weight residual 108.24 103.10 5.14 1.81e+00 3.05e-01 8.06e+00 ... (remaining 3193 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 7.95: 1028 7.95 - 15.90: 268 15.90 - 23.85: 54 23.85 - 31.80: 18 31.80 - 39.75: 24 Dihedral angle restraints: 1392 sinusoidal: 462 harmonic: 930 Sorted by residual: dihedral pdb=" CA ALA A 91 " pdb=" C ALA A 91 " pdb=" N THR A 92 " pdb=" CA THR A 92 " ideal model delta harmonic sigma weight residual -180.00 -166.25 -13.75 0 5.00e+00 4.00e-02 7.57e+00 dihedral pdb=" CA ALA D 91 " pdb=" C ALA D 91 " pdb=" N THR D 92 " pdb=" CA THR D 92 " ideal model delta harmonic sigma weight residual -180.00 -166.27 -13.73 0 5.00e+00 4.00e-02 7.54e+00 dihedral pdb=" CA ALA F 91 " pdb=" C ALA F 91 " pdb=" N THR F 92 " pdb=" CA THR F 92 " ideal model delta harmonic sigma weight residual 180.00 -166.27 -13.73 0 5.00e+00 4.00e-02 7.54e+00 ... (remaining 1389 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.026: 171 0.026 - 0.052: 106 0.052 - 0.078: 72 0.078 - 0.103: 33 0.103 - 0.129: 44 Chirality restraints: 426 Sorted by residual: chirality pdb=" CA VAL F 71 " pdb=" N VAL F 71 " pdb=" C VAL F 71 " pdb=" CB VAL F 71 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.16e-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 2.57 -0.13 2.00e-01 2.50e+01 4.14e-01 chirality pdb=" CA VAL B 71 " pdb=" N VAL B 71 " pdb=" C VAL B 71 " pdb=" CB VAL B 71 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 423 not shown) Planarity restraints: 396 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLU E 83 " -0.004 2.00e-02 2.50e+03 7.27e-03 5.28e-01 pdb=" C GLU E 83 " 0.013 2.00e-02 2.50e+03 pdb=" O GLU E 83 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY E 84 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU F 83 " 0.004 2.00e-02 2.50e+03 7.13e-03 5.09e-01 pdb=" C GLU F 83 " -0.012 2.00e-02 2.50e+03 pdb=" O GLU F 83 " 0.005 2.00e-02 2.50e+03 pdb=" N GLY F 84 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU D 83 " -0.004 2.00e-02 2.50e+03 7.10e-03 5.04e-01 pdb=" C GLU D 83 " 0.012 2.00e-02 2.50e+03 pdb=" O GLU D 83 " -0.005 2.00e-02 2.50e+03 pdb=" N GLY D 84 " -0.004 2.00e-02 2.50e+03 ... (remaining 393 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 499 2.80 - 3.32: 2053 3.32 - 3.85: 3686 3.85 - 4.37: 3947 4.37 - 4.90: 7981 Nonbonded interactions: 18166 Sorted by model distance: nonbonded pdb=" NZ LYS E 60 " pdb=" OE1 GLN E 62 " model vdw 2.275 2.520 nonbonded pdb=" NZ LYS D 60 " pdb=" OE1 GLN D 62 " model vdw 2.275 2.520 nonbonded pdb=" NZ LYS C 60 " pdb=" OE1 GLN C 62 " model vdw 2.276 2.520 nonbonded pdb=" NZ LYS B 60 " pdb=" OE1 GLN B 62 " model vdw 2.276 2.520 nonbonded pdb=" NZ LYS A 60 " pdb=" OE1 GLN A 62 " model vdw 2.276 2.520 ... (remaining 18161 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: 1.060 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.730 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.230 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6714 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 : 0.004 0.019 2370 Z= 0.264 Angle : 0.590 5.180 3198 Z= 0.360 Chirality : 0.056 0.129 426 Planarity : 0.002 0.007 396 Dihedral : 11.350 39.754 804 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.93 % Favored : 91.07 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -5.55 (0.24), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.23 (0.18), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS F 50 PHE 0.006 0.003 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 8 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 8 time to evaluate : 0.263 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 8 average time/residue: 0.1220 time to fit residues: 1.5746 Evaluate side-chains 3 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 3 time to evaluate : 0.243 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3526 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 15 optimal weight: 10.0000 chunk 23 optimal weight: 8.9990 chunk 9 optimal weight: 9.9990 chunk 14 optimal weight: 6.9990 chunk 17 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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: 0.6839 moved from start: 0.1214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2370 Z= 0.292 Angle : 0.525 4.870 3198 Z= 0.313 Chirality : 0.057 0.128 426 Planarity : 0.003 0.017 396 Dihedral : 5.443 13.628 342 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.04 % Favored : 91.96 % Rotamer: Outliers : 1.25 % Allowed : 5.83 % Favored : 92.92 % 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: -5.34 (0.27), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.07 (0.21), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS D 50 PHE 0.004 0.002 PHE A 94 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 7 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 4 time to evaluate : 0.264 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 7 average time/residue: 0.0596 time to fit residues: 0.9725 Evaluate side-chains 6 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 3 time to evaluate : 0.258 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0250 time to fit residues: 0.4695 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 10.0000 chunk 18 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 27 optimal weight: 3.9990 chunk 29 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 9 optimal weight: 10.0000 chunk 21 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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: 0.6999 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 2370 Z= 0.426 Angle : 0.622 5.093 3198 Z= 0.371 Chirality : 0.060 0.144 426 Planarity : 0.004 0.015 396 Dihedral : 6.192 15.520 342 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.69 % Favored : 86.31 % Rotamer: Outliers : 4.17 % Allowed : 4.58 % Favored : 91.25 % 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: -5.01 (0.31), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.81 (0.24), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.005 HIS A 50 PHE 0.006 0.002 PHE D 94 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 21 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 11 time to evaluate : 0.263 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 19 average time/residue: 0.0749 time to fit residues: 2.2129 Evaluate side-chains 16 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 10 time to evaluate : 0.260 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0294 time to fit residues: 0.6328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 6.9990 chunk 18 optimal weight: 8.9990 chunk 27 optimal weight: 6.9990 chunk 28 optimal weight: 5.9990 chunk 14 optimal weight: 7.9990 chunk 25 optimal weight: 10.0000 chunk 7 optimal weight: 9.9990 chunk 24 optimal weight: 6.9990 chunk 16 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 overall best weight: 4.5788 ------------------------------------------------------------------------------- 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: 0.7007 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 2370 Z= 0.348 Angle : 0.554 4.832 3198 Z= 0.331 Chirality : 0.057 0.134 426 Planarity : 0.003 0.012 396 Dihedral : 5.749 14.231 342 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 14.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.99 % Favored : 86.01 % Rotamer: Outliers : 1.25 % Allowed : 7.92 % Favored : 90.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.33), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.25), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS D 50 PHE 0.017 0.004 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 9 time to evaluate : 0.316 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 12 average time/residue: 0.0872 time to fit residues: 1.7620 Evaluate side-chains 11 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 8 time to evaluate : 0.268 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0281 time to fit residues: 0.5202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 20.0000 chunk 11 optimal weight: 6.9990 chunk 24 optimal weight: 6.9990 chunk 20 optimal weight: 7.9990 chunk 0 optimal weight: 10.0000 chunk 14 optimal weight: 0.0970 chunk 26 optimal weight: 9.9990 chunk 7 optimal weight: 10.0000 chunk 9 optimal weight: 5.9990 chunk 5 optimal weight: 10.0000 chunk 17 optimal weight: 10.0000 overall best weight: 5.6186 ------------------------------------------------------------------------------- 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: 0.7068 moved from start: 0.3214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.026 2370 Z= 0.396 Angle : 0.603 5.007 3198 Z= 0.362 Chirality : 0.059 0.141 426 Planarity : 0.003 0.012 396 Dihedral : 6.055 14.338 342 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 14.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.75 % Favored : 81.25 % Rotamer: Outliers : 2.08 % Allowed : 9.58 % Favored : 88.33 % 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: -5.05 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.84 (0.26), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.005 HIS A 50 PHE 0.019 0.004 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 8 time to evaluate : 0.250 Fit side-chains outliers start: 5 outliers final: 5 residues processed: 12 average time/residue: 0.0915 time to fit residues: 1.7750 Evaluate side-chains 12 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 7 time to evaluate : 0.269 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0325 time to fit residues: 0.6161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 29 optimal weight: 10.0000 chunk 24 optimal weight: 3.9990 chunk 13 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 27 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 chunk 16 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 2370 Z= 0.288 Angle : 0.508 4.603 3198 Z= 0.305 Chirality : 0.056 0.130 426 Planarity : 0.002 0.010 396 Dihedral : 5.532 13.626 342 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 13.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.29 % Favored : 85.71 % Rotamer: Outliers : 0.42 % Allowed : 9.17 % Favored : 90.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.91 (0.35), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.27), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS A 50 PHE 0.012 0.003 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 13 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 12 time to evaluate : 0.264 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 13 average time/residue: 0.0746 time to fit residues: 1.6350 Evaluate side-chains 10 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.263 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 11 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.0170 overall best weight: 2.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6976 moved from start: 0.3341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2370 Z= 0.192 Angle : 0.436 4.094 3198 Z= 0.262 Chirality : 0.054 0.129 426 Planarity : 0.002 0.010 396 Dihedral : 4.962 13.021 342 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 0.00 % Allowed : 12.08 % Favored : 87.92 % 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: -4.65 (0.36), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS A 50 PHE 0.009 0.002 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 12 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 12 time to evaluate : 0.272 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 12 average time/residue: 0.0870 time to fit residues: 1.7247 Evaluate side-chains 11 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.256 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 26 optimal weight: 9.9990 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 10.0000 chunk 16 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 24 optimal weight: 10.0000 chunk 17 optimal weight: 3.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- 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: 0.7023 moved from start: 0.3446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2370 Z= 0.278 Angle : 0.487 4.593 3198 Z= 0.294 Chirality : 0.056 0.131 426 Planarity : 0.002 0.010 396 Dihedral : 5.267 13.339 342 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 16.07 % Favored : 83.93 % Rotamer: Outliers : 0.00 % Allowed : 13.75 % Favored : 86.25 % 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: -4.67 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.004 HIS D 50 PHE 0.014 0.003 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 11 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 11 time to evaluate : 0.281 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 11 average time/residue: 0.0813 time to fit residues: 1.5419 Evaluate side-chains 10 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 10 time to evaluate : 0.262 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 6.9990 chunk 17 optimal weight: 5.9990 chunk 13 optimal weight: 5.9990 chunk 19 optimal weight: 0.0870 chunk 29 optimal weight: 10.0000 chunk 27 optimal weight: 10.0000 chunk 23 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 10.0000 overall best weight: 3.4166 ------------------------------------------------------------------------------- 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: 0.7020 moved from start: 0.3522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2370 Z= 0.258 Angle : 0.475 4.449 3198 Z= 0.287 Chirality : 0.055 0.132 426 Planarity : 0.002 0.010 396 Dihedral : 5.241 13.356 342 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 12.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.10 % Favored : 86.90 % Rotamer: Outliers : 0.42 % Allowed : 14.17 % Favored : 85.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.38), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.29), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS D 50 PHE 0.013 0.003 PHE F 94 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 9 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.266 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 9 average time/residue: 0.0742 time to fit residues: 1.2323 Evaluate side-chains 9 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 8 time to evaluate : 0.230 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0240 time to fit residues: 0.3484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 10.0000 chunk 21 optimal weight: 7.9990 chunk 3 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 23 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 24 optimal weight: 5.9990 chunk 4 optimal weight: 6.9990 chunk 20 optimal weight: 10.0000 chunk 1 optimal weight: 7.9990 chunk 17 optimal weight: 4.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- 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: 0.7105 moved from start: 0.3688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.034 2370 Z= 0.447 Angle : 0.625 5.071 3198 Z= 0.377 Chirality : 0.059 0.147 426 Planarity : 0.003 0.011 396 Dihedral : 6.022 15.003 342 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.21 % Favored : 76.79 % Rotamer: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.84 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS A 50 PHE 0.019 0.005 PHE F 94 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 6 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.232 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 6 average time/residue: 0.0955 time to fit residues: 1.0691 Evaluate side-chains 6 residues out of total 240 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 6 time to evaluate : 0.231 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 6.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 chunk 18 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 5.9990 chunk 29 optimal weight: 0.0770 chunk 1 optimal weight: 6.9990 chunk 28 optimal weight: 2.9990 overall best weight: 2.0146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 65 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.152999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.129512 restraints weight = 4310.586| |-----------------------------------------------------------------------------| r_work (start): 0.4800 rms_B_bonded: 3.31 r_work: 0.4711 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6088 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2370 Z= 0.185 Angle : 0.444 4.082 3198 Z= 0.266 Chirality : 0.055 0.132 426 Planarity : 0.002 0.010 396 Dihedral : 5.114 12.913 342 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer: Outliers : 0.00 % Allowed : 14.17 % Favored : 85.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.65 (0.37), residues: 336 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.28), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS D 50 PHE 0.009 0.002 PHE B 94 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 815.49 seconds wall clock time: 16 minutes 18.20 seconds (978.20 seconds total)