Starting phenix.real_space_refine on Thu Dec 7 16:34:28 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/12_2023/7xo2_33334.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/12_2023/7xo2_33334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/12_2023/7xo2_33334.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/12_2023/7xo2_33334.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/12_2023/7xo2_33334.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xo2_33334/12_2023/7xo2_33334.pdb" } resolution = 3.0 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 1602 2.51 5 N 444 2.21 5 O 504 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "I TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 61": "OE1" <-> "OE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 61": "OE1" <-> "OE2" Residue "D TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 61": "OE1" <-> "OE2" Residue "A TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 61": "OE1" <-> "OE2" Residue "E TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 61": "OE1" <-> "OE2" Residue "B TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 61": "OE1" <-> "OE2" 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: 2550 Number of models: 1 Model: "" Number of chains: 6 Chain: "I" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "C" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "D" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "A" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "E" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Chain: "B" Number of atoms: 425 Number of conformers: 1 Conformer: "" Number of residues, atoms: 62, 425 Classifications: {'peptide': 62} Link IDs: {'TRANS': 61} Time building chain proxies: 1.62, per 1000 atoms: 0.64 Number of scatterers: 2550 At special positions: 0 Unit cell: (96.46, 94.34, 33.92, 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 504 8.00 N 444 7.00 C 1602 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: 0.98 Conformation dependent library (CDL) restraints added in 514.2 milliseconds 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 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 16 sheets defined 0.0% alpha, 56.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'I' and resid 37 through 45 removed outlier: 6.598A pdb=" N VAL D 37 " --> pdb=" O LEU E 38 " (cutoff:3.500A) removed outlier: 7.929A pdb=" N VAL E 40 " --> pdb=" O VAL D 37 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR D 39 " --> pdb=" O VAL E 40 " (cutoff:3.500A) removed outlier: 7.900A pdb=" N SER E 42 " --> pdb=" O TYR D 39 " (cutoff:3.500A) removed outlier: 6.472A pdb=" N GLY D 41 " --> pdb=" O SER E 42 " (cutoff:3.500A) removed outlier: 7.734A pdb=" N THR E 44 " --> pdb=" O GLY D 41 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N LYS D 43 " --> pdb=" O THR E 44 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'I' and resid 48 through 57 removed outlier: 6.639A pdb=" N VAL I 48 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.959A pdb=" N GLY D 51 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 8.596A pdb=" N HIS I 50 " --> pdb=" O GLY D 51 " (cutoff:3.500A) removed outlier: 6.788A pdb=" N ALA D 53 " --> pdb=" O HIS I 50 " (cutoff:3.500A) removed outlier: 9.260A pdb=" N VAL I 52 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 10.566A pdb=" N VAL D 55 " --> pdb=" O VAL I 52 " (cutoff:3.500A) removed outlier: 9.252A pdb=" N THR I 54 " --> pdb=" O VAL D 55 " (cutoff:3.500A) removed outlier: 10.271A pdb=" N GLU D 57 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 8.929A pdb=" N ALA I 56 " --> pdb=" O GLU D 57 " (cutoff:3.500A) removed outlier: 6.966A pdb=" N VAL D 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 7.018A pdb=" N HIS E 50 " --> pdb=" O VAL D 49 " (cutoff:3.500A) removed outlier: 7.026A pdb=" N GLY D 51 " --> pdb=" O HIS E 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'I' and resid 61 through 66 removed outlier: 6.349A pdb=" N GLU I 61 " --> pdb=" O GLN D 62 " (cutoff:3.500A) removed outlier: 7.716A pdb=" N THR D 64 " --> pdb=" O GLU I 61 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N VAL I 63 " --> pdb=" O THR D 64 " (cutoff:3.500A) removed outlier: 7.630A pdb=" N VAL D 66 " --> pdb=" O VAL I 63 " (cutoff:3.500A) removed outlier: 6.113A pdb=" N ASN I 65 " --> pdb=" O VAL D 66 " (cutoff:3.500A) removed outlier: 6.274A pdb=" N GLU D 61 " --> pdb=" O GLN E 62 " (cutoff:3.500A) removed outlier: 7.654A pdb=" N THR E 64 " --> pdb=" O GLU D 61 " (cutoff:3.500A) removed outlier: 6.277A pdb=" N VAL D 63 " --> pdb=" O THR E 64 " (cutoff:3.500A) removed outlier: 7.578A pdb=" N VAL E 66 " --> pdb=" O VAL D 63 " (cutoff:3.500A) removed outlier: 6.074A pdb=" N ASN D 65 " --> pdb=" O VAL E 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'I' and resid 69 through 72 Processing sheet with id=AA5, first strand: chain 'I' and resid 75 through 79 Processing sheet with id=AA6, first strand: chain 'I' and resid 82 through 83 removed outlier: 6.488A pdb=" N VAL I 82 " --> pdb=" O GLU D 83 " (cutoff:3.500A) removed outlier: 6.567A pdb=" N VAL D 82 " --> pdb=" O GLU E 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'I' and resid 87 through 88 Processing sheet with id=AA8, first strand: chain 'I' and resid 92 through 96 Processing sheet with id=AA9, first strand: chain 'C' and resid 37 through 45 removed outlier: 6.631A pdb=" N VAL C 37 " --> pdb=" O LEU A 38 " (cutoff:3.500A) removed outlier: 7.953A pdb=" N VAL A 40 " --> pdb=" O VAL C 37 " (cutoff:3.500A) removed outlier: 6.463A pdb=" N TYR C 39 " --> pdb=" O VAL A 40 " (cutoff:3.500A) removed outlier: 7.918A pdb=" N SER A 42 " --> pdb=" O TYR C 39 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N GLY C 41 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 7.745A pdb=" N THR A 44 " --> pdb=" O GLY C 41 " (cutoff:3.500A) removed outlier: 6.271A pdb=" N LYS C 43 " --> pdb=" O THR A 44 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N VAL A 37 " --> pdb=" O LEU B 38 " (cutoff:3.500A) removed outlier: 7.917A pdb=" N VAL B 40 " --> pdb=" O VAL A 37 " (cutoff:3.500A) removed outlier: 6.432A pdb=" N TYR A 39 " --> pdb=" O VAL B 40 " (cutoff:3.500A) removed outlier: 7.901A pdb=" N SER B 42 " --> pdb=" O TYR A 39 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N GLY A 41 " --> pdb=" O SER B 42 " (cutoff:3.500A) removed outlier: 7.730A pdb=" N THR B 44 " --> pdb=" O GLY A 41 " (cutoff:3.500A) removed outlier: 6.264A pdb=" N LYS A 43 " --> pdb=" O THR B 44 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 48 through 57 removed outlier: 6.946A pdb=" N VAL C 49 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N HIS A 50 " --> pdb=" O VAL C 49 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N GLY C 51 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N VAL A 48 " --> pdb=" O VAL B 49 " (cutoff:3.500A) removed outlier: 7.944A pdb=" N GLY B 51 " --> pdb=" O VAL A 48 " (cutoff:3.500A) removed outlier: 8.566A pdb=" N HIS A 50 " --> pdb=" O GLY B 51 " (cutoff:3.500A) removed outlier: 6.754A pdb=" N ALA B 53 " --> pdb=" O HIS A 50 " (cutoff:3.500A) removed outlier: 9.208A pdb=" N VAL A 52 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 10.509A pdb=" N VAL B 55 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 9.186A pdb=" N THR A 54 " --> pdb=" O VAL B 55 " (cutoff:3.500A) removed outlier: 10.201A pdb=" N GLU B 57 " --> pdb=" O THR A 54 " (cutoff:3.500A) removed outlier: 8.848A pdb=" N ALA A 56 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 61 through 66 removed outlier: 6.250A pdb=" N GLU C 61 " --> pdb=" O GLN A 62 " (cutoff:3.500A) removed outlier: 7.643A pdb=" N THR A 64 " --> pdb=" O GLU C 61 " (cutoff:3.500A) removed outlier: 6.267A pdb=" N VAL C 63 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 7.576A pdb=" N VAL A 66 " --> pdb=" O VAL C 63 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N ASN C 65 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.320A pdb=" N GLU A 61 " --> pdb=" O GLN B 62 " (cutoff:3.500A) removed outlier: 7.697A pdb=" N THR B 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 6.313A pdb=" N VAL A 63 " --> pdb=" O THR B 64 " (cutoff:3.500A) removed outlier: 7.616A pdb=" N VAL B 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 6.102A pdb=" N ASN A 65 " --> pdb=" O VAL B 66 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'C' and resid 69 through 72 Processing sheet with id=AB4, first strand: chain 'C' and resid 75 through 79 Processing sheet with id=AB5, first strand: chain 'C' and resid 82 through 83 removed outlier: 6.573A pdb=" N VAL C 82 " --> pdb=" O GLU A 83 " (cutoff:3.500A) removed outlier: 6.513A pdb=" N VAL A 82 " --> pdb=" O GLU B 83 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB5 Processing sheet with id=AB6, first strand: chain 'C' and resid 87 through 88 Processing sheet with id=AB7, first strand: chain 'C' and resid 92 through 96 68 hydrogen bonds defined for protein. 204 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: 0.59 Time building geometry restraints manager: 1.08 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: 438 1.29 - 1.36: 402 1.36 - 1.42: 102 1.42 - 1.48: 420 1.48 - 1.55: 1200 Bond restraints: 2562 Sorted by residual: bond pdb=" CA LYS A 60 " pdb=" C LYS A 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 3.00e-01 bond pdb=" CA LYS D 60 " pdb=" C LYS D 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.97e-01 bond pdb=" CA LYS C 60 " pdb=" C LYS C 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.72e-01 bond pdb=" CA LYS B 60 " pdb=" C LYS B 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.66e-01 bond pdb=" CA LYS E 60 " pdb=" C LYS E 60 " ideal model delta sigma weight residual 1.522 1.527 -0.005 9.30e-03 1.16e+04 2.53e-01 ... (remaining 2557 not shown) Histogram of bond angle deviations from ideal: 106.07 - 111.11: 1096 111.11 - 116.15: 734 116.15 - 121.19: 833 121.19 - 126.23: 793 126.23 - 131.27: 6 Bond angle restraints: 3462 Sorted by residual: angle pdb=" C THR D 59 " pdb=" N LYS D 60 " pdb=" CA LYS D 60 " ideal model delta sigma weight residual 122.17 120.34 1.83 1.54e+00 4.22e-01 1.42e+00 angle pdb=" C THR C 59 " pdb=" N LYS C 60 " pdb=" CA LYS C 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.40e+00 angle pdb=" C THR B 59 " pdb=" N LYS B 60 " pdb=" CA LYS B 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.40e+00 angle pdb=" C THR E 59 " pdb=" N LYS E 60 " pdb=" CA LYS E 60 " ideal model delta sigma weight residual 122.17 120.35 1.82 1.54e+00 4.22e-01 1.39e+00 angle pdb=" C THR A 59 " pdb=" N LYS A 60 " pdb=" CA LYS A 60 " ideal model delta sigma weight residual 122.17 120.37 1.80 1.54e+00 4.22e-01 1.37e+00 ... (remaining 3457 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.35: 1296 15.35 - 30.70: 96 30.70 - 46.05: 66 46.05 - 61.40: 24 61.40 - 76.75: 6 Dihedral angle restraints: 1488 sinusoidal: 492 harmonic: 996 Sorted by residual: dihedral pdb=" CA GLU C 83 " pdb=" CB GLU C 83 " pdb=" CG GLU C 83 " pdb=" CD GLU C 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.38 -52.62 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA GLU D 83 " pdb=" CB GLU D 83 " pdb=" CG GLU D 83 " pdb=" CD GLU D 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.39 -52.61 3 1.50e+01 4.44e-03 9.13e+00 dihedral pdb=" CA GLU E 83 " pdb=" CB GLU E 83 " pdb=" CG GLU E 83 " pdb=" CD GLU E 83 " ideal model delta sinusoidal sigma weight residual -180.00 -127.41 -52.59 3 1.50e+01 4.44e-03 9.13e+00 ... (remaining 1485 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 227 0.025 - 0.050: 107 0.050 - 0.075: 38 0.075 - 0.100: 17 0.100 - 0.125: 67 Chirality restraints: 456 Sorted by residual: chirality pdb=" CA ILE E 88 " pdb=" N ILE E 88 " pdb=" C ILE E 88 " pdb=" CB ILE E 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA ILE A 88 " pdb=" N ILE A 88 " pdb=" C ILE A 88 " pdb=" CB ILE A 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.79e-01 chirality pdb=" CA ILE B 88 " pdb=" N ILE B 88 " pdb=" C ILE B 88 " pdb=" CB ILE B 88 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.76e-01 ... (remaining 453 not shown) Planarity restraints: 426 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 59 " -0.002 2.00e-02 2.50e+03 4.26e-03 1.81e-01 pdb=" C THR E 59 " 0.007 2.00e-02 2.50e+03 pdb=" O THR E 59 " -0.003 2.00e-02 2.50e+03 pdb=" N LYS E 60 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR C 59 " 0.002 2.00e-02 2.50e+03 4.13e-03 1.70e-01 pdb=" C THR C 59 " -0.007 2.00e-02 2.50e+03 pdb=" O THR C 59 " 0.003 2.00e-02 2.50e+03 pdb=" N LYS C 60 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR D 59 " -0.002 2.00e-02 2.50e+03 4.00e-03 1.60e-01 pdb=" C THR D 59 " 0.007 2.00e-02 2.50e+03 pdb=" O THR D 59 " -0.003 2.00e-02 2.50e+03 pdb=" N LYS D 60 " -0.002 2.00e-02 2.50e+03 ... (remaining 423 not shown) Histogram of nonbonded interaction distances: 2.59 - 3.05: 1576 3.05 - 3.51: 2243 3.51 - 3.97: 3534 3.97 - 4.44: 3796 4.44 - 4.90: 7142 Nonbonded interactions: 18291 Sorted by model distance: nonbonded pdb=" NE2 GLN E 62 " pdb=" OG1 THR E 64 " model vdw 2.586 2.520 nonbonded pdb=" NE2 GLN A 62 " pdb=" OG1 THR A 64 " model vdw 2.586 2.520 nonbonded pdb=" NE2 GLN I 62 " pdb=" OG1 THR I 64 " model vdw 2.586 2.520 nonbonded pdb=" NE2 GLN B 62 " pdb=" OG1 THR B 64 " model vdw 2.586 2.520 nonbonded pdb=" NE2 GLN C 62 " pdb=" OG1 THR C 64 " model vdw 2.587 2.520 ... (remaining 18286 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 'I' } 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: 1.070 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: 4.720 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.620 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:13.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8470 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 : 0.001 0.014 2562 Z= 0.101 Angle : 0.376 2.215 3462 Z= 0.225 Chirality : 0.052 0.125 456 Planarity : 0.001 0.004 426 Dihedral : 18.118 76.747 864 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 0.00 % Allowed : 18.60 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.67 (0.34), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS A 50 PHE 0.002 0.000 PHE B 94 TYR 0.006 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 31 time to evaluate : 0.280 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 31 average time/residue: 1.3684 time to fit residues: 43.4641 Evaluate side-chains 19 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.280 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.3593 ------------------------------------------------------------------------------- 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: 8.9990 chunk 27 optimal weight: 8.9990 chunk 15 optimal weight: 2.9990 chunk 9 optimal weight: 10.0000 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 9.9990 chunk 28 optimal weight: 10.0000 chunk 10 optimal weight: 2.9990 chunk 17 optimal weight: 8.9990 chunk 21 optimal weight: 5.9990 chunk 32 optimal weight: 7.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.8621 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.060 2562 Z= 0.447 Angle : 0.605 7.807 3462 Z= 0.341 Chirality : 0.056 0.140 456 Planarity : 0.003 0.023 426 Dihedral : 4.969 18.874 372 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 6.20 % Allowed : 16.67 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.23 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -0.92 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS D 50 PHE 0.013 0.002 PHE I 94 TYR 0.006 0.002 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 27 time to evaluate : 0.295 Fit side-chains outliers start: 16 outliers final: 6 residues processed: 40 average time/residue: 1.8067 time to fit residues: 73.5523 Evaluate side-chains 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.303 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0273 time to fit residues: 0.4185 ------------------------------------------------------------------------------- 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: 7.9990 chunk 27 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 5.9990 chunk 29 optimal weight: 0.7980 chunk 11 optimal weight: 6.9990 chunk 26 optimal weight: 0.4980 chunk 24 optimal weight: 10.0000 overall best weight: 1.7784 ------------------------------------------------------------------------------- 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: 0.8538 moved from start: 0.2569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2562 Z= 0.204 Angle : 0.469 7.342 3462 Z= 0.267 Chirality : 0.053 0.132 456 Planarity : 0.002 0.017 426 Dihedral : 4.310 14.995 372 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.88 % Allowed : 19.38 % Favored : 76.74 % 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: -1.33 (0.43), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS C 50 PHE 0.007 0.002 PHE I 94 TYR 0.009 0.001 TYR E 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 25 time to evaluate : 0.302 Fit side-chains outliers start: 10 outliers final: 5 residues processed: 34 average time/residue: 1.7441 time to fit residues: 60.5240 Evaluate side-chains 24 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 19 time to evaluate : 0.314 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0306 time to fit residues: 0.4349 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 0.0970 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 0.0170 chunk 9 optimal weight: 0.9990 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 overall best weight: 0.6220 ------------------------------------------------------------------------------- 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: 0.8489 moved from start: 0.2407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 2562 Z= 0.121 Angle : 0.416 7.560 3462 Z= 0.237 Chirality : 0.053 0.130 456 Planarity : 0.001 0.014 426 Dihedral : 3.792 13.081 372 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 2.71 % Allowed : 21.71 % Favored : 75.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.44), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.00 (0.33), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS E 50 PHE 0.005 0.001 PHE C 94 TYR 0.008 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 25 time to evaluate : 0.288 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 31 average time/residue: 1.5091 time to fit residues: 47.8403 Evaluate side-chains 27 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 22 time to evaluate : 0.287 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0268 time to fit residues: 0.4089 ------------------------------------------------------------------------------- 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: 9.9990 chunk 14 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 7.9990 chunk 17 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 8 optimal weight: 10.0000 chunk 11 optimal weight: 8.9990 chunk 6 optimal weight: 10.0000 chunk 20 optimal weight: 5.9990 overall best weight: 8.1990 ------------------------------------------------------------------------------- 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: 0.8644 moved from start: 0.3256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.011 0.061 2562 Z= 0.722 Angle : 0.710 8.139 3462 Z= 0.406 Chirality : 0.061 0.171 456 Planarity : 0.003 0.015 426 Dihedral : 5.917 23.974 372 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.28 % Favored : 89.72 % Rotamer: Outliers : 5.04 % Allowed : 20.54 % Favored : 74.42 % 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: -1.54 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.17 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.003 HIS C 50 PHE 0.012 0.003 PHE A 94 TYR 0.010 0.003 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 28 time to evaluate : 0.289 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 38 average time/residue: 1.8516 time to fit residues: 71.5454 Evaluate side-chains 35 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.292 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 6 residues processed: 2 average time/residue: 1.4108 time to fit residues: 3.2298 ------------------------------------------------------------------------------- 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: 2.9990 chunk 34 optimal weight: 0.9980 chunk 28 optimal weight: 6.9990 chunk 16 optimal weight: 1.9990 chunk 2 optimal weight: 7.9990 chunk 11 optimal weight: 2.9990 chunk 18 optimal weight: 7.9990 chunk 33 optimal weight: 0.9990 chunk 3 optimal weight: 6.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 4.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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: 0.8566 moved from start: 0.2875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 2562 Z= 0.225 Angle : 0.480 7.065 3462 Z= 0.276 Chirality : 0.053 0.131 456 Planarity : 0.002 0.012 426 Dihedral : 4.820 17.394 372 Min Nonbonded Distance : 2.322 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer: Outliers : 2.71 % Allowed : 22.48 % Favored : 74.81 % 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: -1.58 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.19 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.002 HIS C 50 PHE 0.008 0.002 PHE C 94 TYR 0.007 0.001 TYR D 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 24 time to evaluate : 0.314 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 30 average time/residue: 1.7850 time to fit residues: 54.6327 Evaluate side-chains 26 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 20 time to evaluate : 0.297 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0267 time to fit residues: 0.4255 ------------------------------------------------------------------------------- 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: 10.0000 chunk 29 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 6 optimal weight: 10.0000 chunk 22 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 2562 Z= 0.329 Angle : 0.519 7.345 3462 Z= 0.298 Chirality : 0.054 0.131 456 Planarity : 0.002 0.012 426 Dihedral : 5.031 18.681 372 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 5.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.89 % Favored : 91.11 % Rotamer: Outliers : 3.88 % Allowed : 23.26 % Favored : 72.87 % 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: -1.60 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.21 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.009 0.002 PHE I 94 TYR 0.009 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 28 time to evaluate : 0.307 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 36 average time/residue: 1.8556 time to fit residues: 67.9932 Evaluate side-chains 35 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 28 time to evaluate : 0.271 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.6806 time to fit residues: 1.7299 ------------------------------------------------------------------------------- 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: 5.9990 chunk 3 optimal weight: 8.9990 chunk 27 optimal weight: 7.9990 chunk 31 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 32 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 9 optimal weight: 8.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- 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: 0.8611 moved from start: 0.3044 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.047 2562 Z= 0.427 Angle : 0.588 7.776 3462 Z= 0.338 Chirality : 0.056 0.146 456 Planarity : 0.002 0.012 426 Dihedral : 5.399 20.677 372 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.78 % Favored : 92.22 % Rotamer: Outliers : 3.88 % Allowed : 22.87 % Favored : 73.26 % 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: -1.62 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS C 50 PHE 0.010 0.002 PHE I 94 TYR 0.007 0.001 TYR I 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 30 time to evaluate : 0.298 Fit side-chains outliers start: 10 outliers final: 8 residues processed: 38 average time/residue: 1.8601 time to fit residues: 71.8858 Evaluate side-chains 38 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 30 time to evaluate : 0.266 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 7 residues processed: 1 average time/residue: 0.0255 time to fit residues: 0.3852 ------------------------------------------------------------------------------- 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: 0.0670 chunk 30 optimal weight: 9.9990 chunk 32 optimal weight: 8.9990 chunk 21 optimal weight: 8.9990 chunk 34 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 overall best weight: 2.0124 ------------------------------------------------------------------------------- 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: 0.8560 moved from start: 0.2901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2562 Z= 0.224 Angle : 0.492 7.655 3462 Z= 0.279 Chirality : 0.054 0.136 456 Planarity : 0.002 0.013 426 Dihedral : 4.705 16.515 372 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 3.10 % Allowed : 24.03 % Favored : 72.87 % 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: -1.62 (0.42), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.22 (0.32), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS D 50 PHE 0.007 0.002 PHE C 94 TYR 0.009 0.001 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 25 time to evaluate : 0.312 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 32 average time/residue: 1.7698 time to fit residues: 57.7533 Evaluate side-chains 29 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 24 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.3882 ------------------------------------------------------------------------------- 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: 8.9990 chunk 22 optimal weight: 4.9990 chunk 17 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 8 optimal weight: 6.9990 chunk 26 optimal weight: 4.9990 chunk 4 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 11 optimal weight: 6.9990 chunk 29 optimal weight: 6.9990 overall best weight: 5.9990 ------------------------------------------------------------------------------- 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: 0.8631 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.053 2562 Z= 0.544 Angle : 0.638 8.119 3462 Z= 0.365 Chirality : 0.058 0.151 456 Planarity : 0.003 0.013 426 Dihedral : 5.699 22.260 372 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.72 % Favored : 90.28 % Rotamer: Outliers : 2.71 % Allowed : 24.42 % Favored : 72.87 % 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: -1.65 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.25 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS C 50 PHE 0.011 0.003 PHE I 94 TYR 0.007 0.002 TYR I 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 720 Ramachandran restraints generated. 360 Oldfield, 0 Emsley, 360 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 29 time to evaluate : 0.300 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 1.8137 time to fit residues: 66.4463 Evaluate side-chains 34 residues out of total 258 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 28 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.3396 ------------------------------------------------------------------------------- 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: 1.9990 chunk 5 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 24 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 22 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3488 r_free = 0.3488 target = 0.092878 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.083228 restraints weight = 4584.110| |-----------------------------------------------------------------------------| r_work (start): 0.3332 rms_B_bonded: 1.96 r_work: 0.3249 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.3157 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3157 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 2562 Z= 0.356 Angle : 0.572 8.740 3462 Z= 0.325 Chirality : 0.055 0.143 456 Planarity : 0.002 0.013 426 Dihedral : 5.267 20.487 372 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.22 % Favored : 92.78 % Rotamer: Outliers : 3.49 % Allowed : 23.64 % Favored : 72.87 % 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: -1.69 (0.41), residues: 360 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.28 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.002 HIS C 50 PHE 0.009 0.002 PHE I 94 TYR 0.009 0.002 TYR B 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1426.90 seconds wall clock time: 26 minutes 17.13 seconds (1577.13 seconds total)