Starting phenix.real_space_refine on Fri Aug 2 16:46:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r47_18881/08_2024/8r47_18881.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r47_18881/08_2024/8r47_18881.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r47_18881/08_2024/8r47_18881.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r47_18881/08_2024/8r47_18881.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r47_18881/08_2024/8r47_18881.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8r47_18881/08_2024/8r47_18881.cif" } resolution = 2.25 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 2376 2.51 5 N 636 2.21 5 O 756 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 80": "OE1" <-> "OE2" Residue "A ASP 81": "OD1" <-> "OD2" Residue "A PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 80": "OE1" <-> "OE2" Residue "B ASP 81": "OD1" <-> "OD2" Residue "B PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "C ASP 81": "OD1" <-> "OD2" Residue "C PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 80": "OE1" <-> "OE2" Residue "D ASP 81": "OD1" <-> "OD2" Residue "D PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 80": "OE1" <-> "OE2" Residue "E ASP 81": "OD1" <-> "OD2" Residue "E PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 80": "OE1" <-> "OE2" Residue "F ASP 81": "OD1" <-> "OD2" Residue "F PHE 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3780 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Chain: "B" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Chain: "C" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Chain: "D" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Chain: "E" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Chain: "F" Number of atoms: 630 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 630 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 2, 'TRANS': 80} Chain breaks: 1 Time building chain proxies: 2.76, per 1000 atoms: 0.73 Number of scatterers: 3780 At special positions: 0 Unit cell: (77.522, 81.258, 45.766, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 756 8.00 N 636 7.00 C 2376 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 87 " distance=2.04 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 87 " distance=2.04 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 87 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 87 " distance=2.04 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 87 " distance=2.04 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 87 " distance=2.04 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: 1.28 Conformation dependent library (CDL) restraints added in 678.1 milliseconds 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 864 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 32.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.53 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 16 through 22 removed outlier: 6.776A pdb=" N CYS B 22 " --> pdb=" O THR A 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS C 22 " --> pdb=" O THR B 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS D 22 " --> pdb=" O THR C 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS E 22 " --> pdb=" O THR D 21 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N CYS F 22 " --> pdb=" O THR E 21 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 26 through 31 removed outlier: 6.803A pdb=" N LEU A 27 " --> pdb=" O SER B 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG B 28 " --> pdb=" O LEU A 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU B 27 " --> pdb=" O SER C 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG C 28 " --> pdb=" O LEU B 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU C 27 " --> pdb=" O SER D 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG D 28 " --> pdb=" O LEU C 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU D 27 " --> pdb=" O SER E 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG E 28 " --> pdb=" O LEU D 27 " (cutoff:3.500A) removed outlier: 6.803A pdb=" N LEU E 27 " --> pdb=" O SER F 26 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ARG F 28 " --> pdb=" O LEU E 27 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 34 through 37 removed outlier: 6.409A pdb=" N TYR A 35 " --> pdb=" O GLN B 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR B 35 " --> pdb=" O GLN C 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR C 35 " --> pdb=" O GLN D 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR D 35 " --> pdb=" O GLN E 36 " (cutoff:3.500A) removed outlier: 6.409A pdb=" N TYR E 35 " --> pdb=" O GLN F 36 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 44 through 48 removed outlier: 6.591A pdb=" N LEU A 44 " --> pdb=" O LEU B 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE B 47 " --> pdb=" O LEU A 44 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL A 46 " --> pdb=" O ILE B 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU B 44 " --> pdb=" O LEU C 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE C 47 " --> pdb=" O LEU B 44 " (cutoff:3.500A) removed outlier: 9.152A pdb=" N VAL B 46 " --> pdb=" O ILE C 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU C 44 " --> pdb=" O LEU D 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE D 47 " --> pdb=" O LEU C 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL C 46 " --> pdb=" O ILE D 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU D 44 " --> pdb=" O LEU E 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE E 47 " --> pdb=" O LEU D 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL D 46 " --> pdb=" O ILE E 47 " (cutoff:3.500A) removed outlier: 6.591A pdb=" N LEU E 44 " --> pdb=" O LEU F 45 " (cutoff:3.500A) removed outlier: 8.009A pdb=" N ILE F 47 " --> pdb=" O LEU E 44 " (cutoff:3.500A) removed outlier: 9.151A pdb=" N VAL E 46 " --> pdb=" O ILE F 47 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 69 through 74 removed outlier: 6.542A pdb=" N ALA A 70 " --> pdb=" O SER B 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR B 73 " --> pdb=" O ALA A 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU A 72 " --> pdb=" O THR B 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA B 70 " --> pdb=" O SER C 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR C 73 " --> pdb=" O ALA B 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU B 72 " --> pdb=" O THR C 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA C 70 " --> pdb=" O SER D 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR D 73 " --> pdb=" O ALA C 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU C 72 " --> pdb=" O THR D 73 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N ALA D 70 " --> pdb=" O SER E 71 " (cutoff:3.500A) removed outlier: 7.995A pdb=" N THR E 73 " --> pdb=" O ALA D 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU D 72 " --> pdb=" O THR E 73 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N ALA E 70 " --> pdb=" O SER F 71 " (cutoff:3.500A) removed outlier: 7.994A pdb=" N THR F 73 " --> pdb=" O ALA E 70 " (cutoff:3.500A) removed outlier: 6.892A pdb=" N LEU E 72 " --> pdb=" O THR F 73 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 84 through 86 Processing sheet with id=AA7, first strand: chain 'A' and resid 98 through 99 Processing sheet with id=AA8, first strand: chain 'A' and resid 104 through 105 60 hydrogen bonds defined for protein. 180 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: 0.87 Time building geometry restraints manager: 1.44 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 648 1.31 - 1.44: 1116 1.44 - 1.57: 2082 1.57 - 1.69: 0 1.69 - 1.82: 12 Bond restraints: 3858 Sorted by residual: bond pdb=" C GLN F 16 " pdb=" O GLN F 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN A 16 " pdb=" O GLN A 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN C 16 " pdb=" O GLN C 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN D 16 " pdb=" O GLN D 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.25e+01 bond pdb=" C GLN B 16 " pdb=" O GLN B 16 " ideal model delta sigma weight residual 1.236 1.182 0.054 1.14e-02 7.69e+03 2.24e+01 ... (remaining 3853 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.77: 234 106.77 - 113.56: 1776 113.56 - 120.36: 1623 120.36 - 127.15: 1551 127.15 - 133.94: 54 Bond angle restraints: 5238 Sorted by residual: angle pdb=" CA GLY E 94 " pdb=" C GLY E 94 " pdb=" O GLY E 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY C 94 " pdb=" C GLY C 94 " pdb=" O GLY C 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY F 94 " pdb=" C GLY F 94 " pdb=" O GLY F 94 " ideal model delta sigma weight residual 121.04 115.87 5.17 7.90e-01 1.60e+00 4.28e+01 angle pdb=" CA GLY A 94 " pdb=" C GLY A 94 " pdb=" O GLY A 94 " ideal model delta sigma weight residual 121.04 115.89 5.15 7.90e-01 1.60e+00 4.24e+01 angle pdb=" CA GLY D 94 " pdb=" C GLY D 94 " pdb=" O GLY D 94 " ideal model delta sigma weight residual 121.04 115.90 5.14 7.90e-01 1.60e+00 4.23e+01 ... (remaining 5233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.00: 1926 16.00 - 32.00: 210 32.00 - 48.00: 42 48.00 - 64.00: 24 64.00 - 80.00: 6 Dihedral angle restraints: 2208 sinusoidal: 828 harmonic: 1380 Sorted by residual: dihedral pdb=" CA PRO D 39 " pdb=" C PRO D 39 " pdb=" N GLY D 40 " pdb=" CA GLY D 40 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO F 39 " pdb=" C PRO F 39 " pdb=" N GLY F 40 " pdb=" CA GLY F 40 " ideal model delta harmonic sigma weight residual -180.00 -162.42 -17.58 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA PRO A 39 " pdb=" C PRO A 39 " pdb=" N GLY A 40 " pdb=" CA GLY A 40 " ideal model delta harmonic sigma weight residual -180.00 -162.43 -17.57 0 5.00e+00 4.00e-02 1.24e+01 ... (remaining 2205 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.083: 399 0.083 - 0.165: 135 0.165 - 0.248: 30 0.248 - 0.330: 6 0.330 - 0.413: 6 Chirality restraints: 576 Sorted by residual: chirality pdb=" CA ILE F 65 " pdb=" N ILE F 65 " pdb=" C ILE F 65 " pdb=" CB ILE F 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.26e+00 chirality pdb=" CA ILE D 65 " pdb=" N ILE D 65 " pdb=" C ILE D 65 " pdb=" CB ILE D 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.24e+00 chirality pdb=" CA ILE C 65 " pdb=" N ILE C 65 " pdb=" C ILE C 65 " pdb=" CB ILE C 65 " both_signs ideal model delta sigma weight residual False 2.43 2.85 -0.41 2.00e-01 2.50e+01 4.24e+00 ... (remaining 573 not shown) Planarity restraints: 672 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 63 " 0.024 2.00e-02 2.50e+03 4.92e-02 2.42e+01 pdb=" C GLY B 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY B 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER B 64 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 63 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLY A 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY A 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER A 64 " 0.029 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 63 " 0.024 2.00e-02 2.50e+03 4.91e-02 2.41e+01 pdb=" C GLY D 63 " -0.085 2.00e-02 2.50e+03 pdb=" O GLY D 63 " 0.032 2.00e-02 2.50e+03 pdb=" N SER D 64 " 0.029 2.00e-02 2.50e+03 ... (remaining 669 not shown) Histogram of nonbonded interaction distances: 2.47 - 2.95: 1806 2.95 - 3.44: 3291 3.44 - 3.93: 7281 3.93 - 4.41: 7950 4.41 - 4.90: 15330 Nonbonded interactions: 35658 Sorted by model distance: nonbonded pdb=" O GLY E 101 " pdb=" O GLY F 100 " model vdw 2.468 3.040 nonbonded pdb=" O GLY C 101 " pdb=" O GLY D 100 " model vdw 2.468 3.040 nonbonded pdb=" O GLY A 101 " pdb=" O GLY B 100 " model vdw 2.468 3.040 nonbonded pdb=" O GLY D 101 " pdb=" O GLY E 100 " model vdw 2.468 3.040 nonbonded pdb=" O GLY B 101 " pdb=" O GLY C 100 " model vdw 2.469 3.040 ... (remaining 35653 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 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: 0.530 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: 0.210 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.100 Find NCS groups from input model: 0.120 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:10.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 27.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 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 : 0.013 0.054 3858 Z= 0.840 Angle : 2.036 9.847 5238 Z= 1.468 Chirality : 0.097 0.413 576 Planarity : 0.016 0.070 672 Dihedral : 15.668 79.999 1326 Min Nonbonded Distance : 2.468 Molprobity Statistics. All-atom Clashscore : 0.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.00 % Allowed : 18.43 % Favored : 81.57 % 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: -4.59 (0.21), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.49 (0.16), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 97 PHE 0.008 0.001 PHE C 61 TYR 0.004 0.001 TYR C 30 ARG 0.002 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.372 Fit side-chains REVERT: B 66 SER cc_start: 0.8301 (p) cc_final: 0.8059 (t) REVERT: D 90 ARG cc_start: 0.6960 (ttm170) cc_final: 0.6716 (ttm-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.5500 time to fit residues: 44.0950 Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 64 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN B 23 GLN ** C 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 23 GLN D 23 GLN E 23 GLN ** F 16 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 23 GLN F 95 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2114 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3858 Z= 0.229 Angle : 0.652 8.081 5238 Z= 0.339 Chirality : 0.045 0.154 576 Planarity : 0.005 0.053 672 Dihedral : 6.156 15.019 534 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 0.76 % Allowed : 15.91 % Favored : 83.33 % 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: -4.15 (0.25), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.15 (0.19), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 97 PHE 0.008 0.002 PHE B 99 TYR 0.011 0.002 TYR B 48 ARG 0.005 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.445 Fit side-chains REVERT: E 90 ARG cc_start: 0.7542 (ttm170) cc_final: 0.7155 (mtt90) REVERT: F 69 THR cc_start: 0.8234 (m) cc_final: 0.7890 (t) outliers start: 3 outliers final: 3 residues processed: 75 average time/residue: 0.5926 time to fit residues: 47.2192 Evaluate side-chains 68 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 65 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 46 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 10.0000 chunk 13 optimal weight: 7.9990 chunk 36 optimal weight: 4.9990 chunk 29 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 0.5980 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 10.0000 chunk 14 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 overall best weight: 3.1188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 16 GLN C 95 ASN F 16 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.2932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 3858 Z= 0.395 Angle : 0.758 6.911 5238 Z= 0.394 Chirality : 0.050 0.173 576 Planarity : 0.006 0.054 672 Dihedral : 6.755 16.095 534 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.27 % Allowed : 15.15 % Favored : 82.58 % 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: -4.08 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.10 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP F 97 PHE 0.010 0.002 PHE F 99 TYR 0.014 0.002 TYR F 48 ARG 0.008 0.002 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.423 Fit side-chains REVERT: D 69 THR cc_start: 0.8361 (m) cc_final: 0.8092 (t) REVERT: D 90 ARG cc_start: 0.7777 (ttm170) cc_final: 0.7552 (mtt180) REVERT: E 80 GLU cc_start: 0.7389 (tt0) cc_final: 0.6977 (tt0) REVERT: F 69 THR cc_start: 0.8240 (m) cc_final: 0.7982 (t) outliers start: 9 outliers final: 7 residues processed: 68 average time/residue: 0.8501 time to fit residues: 60.4739 Evaluate side-chains 65 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 26 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain E residue 103 THR Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 12 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 0 optimal weight: 5.9990 overall best weight: 2.1386 ------------------------------------------------------------------------------- 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: 0.8047 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3858 Z= 0.292 Angle : 0.676 7.479 5238 Z= 0.350 Chirality : 0.047 0.158 576 Planarity : 0.005 0.056 672 Dihedral : 6.494 15.966 534 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.64 % Favored : 95.36 % Rotamer: Outliers : 2.27 % Allowed : 15.91 % Favored : 81.82 % 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: -4.09 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP F 97 PHE 0.007 0.001 PHE B 99 TYR 0.013 0.002 TYR E 48 ARG 0.005 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 62 time to evaluate : 0.450 Fit side-chains REVERT: C 80 GLU cc_start: 0.7479 (tt0) cc_final: 0.7195 (tm-30) REVERT: D 69 THR cc_start: 0.8366 (m) cc_final: 0.8073 (t) REVERT: F 69 THR cc_start: 0.8322 (m) cc_final: 0.8050 (t) REVERT: F 103 THR cc_start: 0.8414 (OUTLIER) cc_final: 0.8070 (m) outliers start: 9 outliers final: 4 residues processed: 68 average time/residue: 0.8729 time to fit residues: 62.0254 Evaluate side-chains 66 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 61 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 46 VAL Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 41 optimal weight: 0.0870 chunk 11 optimal weight: 0.4980 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.3219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3858 Z= 0.146 Angle : 0.566 7.293 5238 Z= 0.290 Chirality : 0.043 0.146 576 Planarity : 0.005 0.055 672 Dihedral : 5.811 14.945 534 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 1.77 % Allowed : 17.17 % Favored : 81.06 % 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: -4.03 (0.26), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.06 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.011 0.001 TYR E 48 ARG 0.001 0.000 ARG A 28 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.443 Fit side-chains REVERT: C 90 ARG cc_start: 0.7500 (ttm170) cc_final: 0.7024 (mmm160) REVERT: D 69 THR cc_start: 0.8398 (m) cc_final: 0.8062 (t) REVERT: F 69 THR cc_start: 0.8247 (m) cc_final: 0.7967 (t) REVERT: F 103 THR cc_start: 0.8385 (OUTLIER) cc_final: 0.8073 (m) outliers start: 7 outliers final: 3 residues processed: 70 average time/residue: 0.7362 time to fit residues: 54.2712 Evaluate side-chains 62 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 8.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 21 optimal weight: 0.0040 chunk 3 optimal weight: 0.0980 chunk 15 optimal weight: 7.9990 chunk 24 optimal weight: 4.9990 chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 0.1980 chunk 26 optimal weight: 3.9990 chunk 33 optimal weight: 4.9990 overall best weight: 1.6596 ------------------------------------------------------------------------------- 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: 0.8033 moved from start: 0.3264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3858 Z= 0.244 Angle : 0.630 5.449 5238 Z= 0.329 Chirality : 0.046 0.153 576 Planarity : 0.005 0.058 672 Dihedral : 6.217 15.224 534 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 2.27 % Allowed : 15.15 % Favored : 82.58 % 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: -3.95 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 97 PHE 0.007 0.001 PHE B 99 TYR 0.012 0.001 TYR A 48 ARG 0.004 0.001 ARG C 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.427 Fit side-chains REVERT: C 80 GLU cc_start: 0.7447 (tt0) cc_final: 0.7137 (tm-30) REVERT: C 90 ARG cc_start: 0.7533 (ttm170) cc_final: 0.7304 (mtp85) REVERT: D 69 THR cc_start: 0.8374 (m) cc_final: 0.8049 (t) REVERT: D 80 GLU cc_start: 0.7523 (OUTLIER) cc_final: 0.7050 (tt0) REVERT: F 69 THR cc_start: 0.8309 (m) cc_final: 0.8023 (t) REVERT: F 103 THR cc_start: 0.8418 (OUTLIER) cc_final: 0.8083 (m) outliers start: 9 outliers final: 4 residues processed: 67 average time/residue: 0.8918 time to fit residues: 62.4001 Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 80 GLU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.0770 chunk 39 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 46 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 21 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.9940 ------------------------------------------------------------------------------- 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: 0.7998 moved from start: 0.3325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3858 Z= 0.174 Angle : 0.588 8.318 5238 Z= 0.302 Chirality : 0.043 0.147 576 Planarity : 0.005 0.057 672 Dihedral : 5.906 14.881 534 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.77 % Allowed : 16.16 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.93 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.99 (0.20), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP F 97 PHE 0.006 0.001 PHE B 99 TYR 0.011 0.001 TYR D 48 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 61 time to evaluate : 0.396 Fit side-chains REVERT: B 90 ARG cc_start: 0.7534 (OUTLIER) cc_final: 0.6939 (mmm-85) REVERT: C 80 GLU cc_start: 0.7388 (tt0) cc_final: 0.7074 (tm-30) REVERT: C 90 ARG cc_start: 0.7583 (ttm170) cc_final: 0.7271 (mtp85) REVERT: D 69 THR cc_start: 0.8401 (m) cc_final: 0.8053 (t) REVERT: F 69 THR cc_start: 0.8299 (m) cc_final: 0.8012 (t) REVERT: F 103 THR cc_start: 0.8399 (OUTLIER) cc_final: 0.8083 (m) outliers start: 7 outliers final: 5 residues processed: 67 average time/residue: 0.8242 time to fit residues: 58.1169 Evaluate side-chains 67 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 60 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 22 optimal weight: 8.9990 chunk 4 optimal weight: 6.9990 chunk 36 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 chunk 44 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 25 optimal weight: 7.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 33 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8040 moved from start: 0.3311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3858 Z= 0.261 Angle : 0.648 7.091 5238 Z= 0.338 Chirality : 0.046 0.154 576 Planarity : 0.005 0.059 672 Dihedral : 6.261 15.785 534 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.02 % Allowed : 16.41 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.88 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.95 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP F 97 PHE 0.007 0.002 PHE B 99 TYR 0.010 0.001 TYR C 48 ARG 0.004 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.451 Fit side-chains REVERT: B 90 ARG cc_start: 0.7596 (OUTLIER) cc_final: 0.6926 (mmm-85) REVERT: C 80 GLU cc_start: 0.7481 (tt0) cc_final: 0.7187 (tm-30) REVERT: C 90 ARG cc_start: 0.7619 (ttm170) cc_final: 0.7343 (mtp85) REVERT: D 69 THR cc_start: 0.8379 (m) cc_final: 0.8043 (t) REVERT: F 69 THR cc_start: 0.8307 (m) cc_final: 0.8023 (t) REVERT: F 103 THR cc_start: 0.8457 (OUTLIER) cc_final: 0.8137 (m) outliers start: 8 outliers final: 5 residues processed: 63 average time/residue: 0.8718 time to fit residues: 57.5101 Evaluate side-chains 63 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 62 SER Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 7.9990 chunk 13 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 0.4980 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 5.9990 chunk 45 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 3.9990 chunk 31 optimal weight: 5.9990 chunk 47 optimal weight: 4.9990 overall best weight: 2.0186 ------------------------------------------------------------------------------- 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: 0.8048 moved from start: 0.3326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3858 Z= 0.283 Angle : 0.670 6.408 5238 Z= 0.349 Chirality : 0.047 0.160 576 Planarity : 0.005 0.060 672 Dihedral : 6.381 16.696 534 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 8.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.33 % Favored : 93.67 % Rotamer: Outliers : 1.52 % Allowed : 17.42 % Favored : 81.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 97 PHE 0.007 0.002 PHE B 99 TYR 0.013 0.001 TYR A 48 ARG 0.004 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.449 Fit side-chains REVERT: B 90 ARG cc_start: 0.7599 (OUTLIER) cc_final: 0.6945 (mmm-85) REVERT: C 80 GLU cc_start: 0.7479 (tt0) cc_final: 0.7186 (tm-30) REVERT: C 90 ARG cc_start: 0.7634 (ttm170) cc_final: 0.7369 (mtp85) REVERT: D 69 THR cc_start: 0.8392 (m) cc_final: 0.8052 (t) REVERT: F 69 THR cc_start: 0.8298 (m) cc_final: 0.8023 (t) outliers start: 6 outliers final: 5 residues processed: 63 average time/residue: 0.9087 time to fit residues: 59.7159 Evaluate side-chains 63 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 8.9990 chunk 38 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 23 optimal weight: 6.9990 chunk 30 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 11 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 5 optimal weight: 7.9990 chunk 10 optimal weight: 1.9990 overall best weight: 2.7788 ------------------------------------------------------------------------------- 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: 0.8070 moved from start: 0.3395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 3858 Z= 0.367 Angle : 0.743 7.389 5238 Z= 0.385 Chirality : 0.049 0.177 576 Planarity : 0.005 0.062 672 Dihedral : 6.634 18.360 534 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.77 % Allowed : 17.93 % Favored : 80.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.87 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 97 PHE 0.008 0.002 PHE B 99 TYR 0.013 0.002 TYR A 48 ARG 0.006 0.001 ARG E 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 948 Ramachandran restraints generated. 474 Oldfield, 0 Emsley, 474 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.424 Fit side-chains REVERT: B 90 ARG cc_start: 0.7597 (OUTLIER) cc_final: 0.6926 (mmm-85) REVERT: C 80 GLU cc_start: 0.7529 (tt0) cc_final: 0.7238 (tm-30) REVERT: C 90 ARG cc_start: 0.7674 (ttm170) cc_final: 0.7392 (mtp85) REVERT: D 69 THR cc_start: 0.8355 (m) cc_final: 0.8045 (t) REVERT: F 69 THR cc_start: 0.8296 (m) cc_final: 0.8036 (t) outliers start: 7 outliers final: 5 residues processed: 64 average time/residue: 0.9236 time to fit residues: 61.6933 Evaluate side-chains 64 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 64 SER Chi-restraints excluded: chain B residue 46 VAL Chi-restraints excluded: chain B residue 90 ARG Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 103 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 2.9990 chunk 39 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 25 optimal weight: 0.9980 chunk 32 optimal weight: 0.8980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4066 r_free = 0.4066 target = 0.141291 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3857 r_free = 0.3857 target = 0.124104 restraints weight = 4082.423| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.39 r_work: 0.3774 rms_B_bonded: 1.82 restraints_weight: 0.5000 r_work: 0.3676 rms_B_bonded: 3.11 restraints_weight: 0.2500 r_work (final): 0.3676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.3406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3858 Z= 0.173 Angle : 0.639 9.949 5238 Z= 0.316 Chirality : 0.044 0.147 576 Planarity : 0.005 0.061 672 Dihedral : 6.027 15.008 534 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.43 % Favored : 95.57 % Rotamer: Outliers : 1.52 % Allowed : 17.93 % Favored : 80.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.86 (0.27), residues: 474 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (0.21), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP B 97 PHE 0.006 0.001 PHE B 99 TYR 0.012 0.001 TYR D 48 ARG 0.002 0.000 ARG A 28 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1739.40 seconds wall clock time: 31 minutes 23.12 seconds (1883.12 seconds total)