Starting phenix.real_space_refine on Sun Mar 10 18:48:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/03_2024/6osm_20186.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/03_2024/6osm_20186.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/03_2024/6osm_20186.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/03_2024/6osm_20186.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/03_2024/6osm_20186.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6osm_20186/03_2024/6osm_20186.pdb" } resolution = 3.4 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= 0.002 sd= 0.009 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 2570 2.51 5 N 710 2.21 5 O 820 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 57": "OE1" <-> "OE2" Residue "A PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 57": "OE1" <-> "OE2" Residue "B PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 57": "OE1" <-> "OE2" Residue "C PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 57": "OE1" <-> "OE2" Residue "D PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 57": "OE1" <-> "OE2" Residue "E PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 57": "OE1" <-> "OE2" Residue "F PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 57": "OE1" <-> "OE2" Residue "G PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 57": "OE1" <-> "OE2" Residue "H PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 57": "OE1" <-> "OE2" Residue "I PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 57": "OE1" <-> "OE2" Residue "J PHE 94": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4100 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "C" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "D" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "E" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "F" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "G" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "H" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "J" Number of atoms: 410 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 410 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'TRANS': 59} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.54, per 1000 atoms: 0.62 Number of scatterers: 4100 At special positions: 0 Unit cell: (100.7, 91.16, 40.28, 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 820 8.00 N 710 7.00 C 2570 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: 1.46 Conformation dependent library (CDL) restraints added in 998.1 milliseconds 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1020 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 46 through 49 removed outlier: 6.493A pdb=" N VAL C 48 " --> pdb=" O GLY A 47 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N VAL A 49 " --> pdb=" O VAL C 48 " (cutoff:3.500A) removed outlier: 6.857A pdb=" N VAL E 48 " --> pdb=" O GLY C 47 " (cutoff:3.500A) removed outlier: 6.951A pdb=" N VAL C 49 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N VAL G 48 " --> pdb=" O GLY E 47 " (cutoff:3.500A) removed outlier: 6.819A pdb=" N VAL E 49 " --> pdb=" O VAL G 48 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 53 through 66 removed outlier: 6.246A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS C 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 59 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N GLN C 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N GLU A 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N THR C 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N VAL A 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N VAL C 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) removed outlier: 6.490A pdb=" N ALA C 53 " --> pdb=" O THR E 54 " (cutoff:3.500A) removed outlier: 8.381A pdb=" N ALA E 56 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N VAL C 55 " --> pdb=" O ALA E 56 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N ALA E 53 " --> pdb=" O THR G 54 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA G 56 " --> pdb=" O ALA E 53 " (cutoff:3.500A) removed outlier: 6.461A pdb=" N VAL E 55 " --> pdb=" O ALA G 56 " (cutoff:3.500A) removed outlier: 6.540A pdb=" N ALA G 53 " --> pdb=" O THR I 54 " (cutoff:3.500A) removed outlier: 8.419A pdb=" N ALA I 56 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 6.498A pdb=" N VAL G 55 " --> pdb=" O ALA I 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 53 through 66 removed outlier: 6.246A pdb=" N ALA A 53 " --> pdb=" O THR C 54 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ALA C 56 " --> pdb=" O ALA A 53 " (cutoff:3.500A) removed outlier: 6.189A pdb=" N VAL A 55 " --> pdb=" O ALA C 56 " (cutoff:3.500A) removed outlier: 7.686A pdb=" N LYS C 58 " --> pdb=" O VAL A 55 " (cutoff:3.500A) removed outlier: 6.177A pdb=" N GLU A 57 " --> pdb=" O LYS C 58 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N LYS C 60 " --> pdb=" O GLU A 57 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N THR A 59 " --> pdb=" O LYS C 60 " (cutoff:3.500A) removed outlier: 10.219A pdb=" N GLN C 62 " --> pdb=" O THR A 59 " (cutoff:3.500A) removed outlier: 8.730A pdb=" N GLU A 61 " --> pdb=" O GLN C 62 " (cutoff:3.500A) removed outlier: 10.581A pdb=" N THR C 64 " --> pdb=" O GLU A 61 " (cutoff:3.500A) removed outlier: 9.124A pdb=" N VAL A 63 " --> pdb=" O THR C 64 " (cutoff:3.500A) removed outlier: 10.281A pdb=" N VAL C 66 " --> pdb=" O VAL A 63 " (cutoff:3.500A) removed outlier: 9.369A pdb=" N ASN A 65 " --> pdb=" O VAL C 66 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 70 through 71 Processing sheet with id=AA5, first strand: chain 'B' and resid 53 through 56 removed outlier: 6.472A pdb=" N ALA B 53 " --> pdb=" O THR D 54 " (cutoff:3.500A) removed outlier: 8.299A pdb=" N ALA D 56 " --> pdb=" O ALA B 53 " (cutoff:3.500A) removed outlier: 6.397A pdb=" N VAL B 55 " --> pdb=" O ALA D 56 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N ALA D 53 " --> pdb=" O THR F 54 " (cutoff:3.500A) removed outlier: 8.450A pdb=" N ALA F 56 " --> pdb=" O ALA D 53 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N VAL D 55 " --> pdb=" O ALA F 56 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N ALA F 53 " --> pdb=" O THR H 54 " (cutoff:3.500A) removed outlier: 8.367A pdb=" N ALA H 56 " --> pdb=" O ALA F 53 " (cutoff:3.500A) removed outlier: 6.445A pdb=" N VAL F 55 " --> pdb=" O ALA H 56 " (cutoff:3.500A) removed outlier: 6.460A pdb=" N ALA H 53 " --> pdb=" O THR J 54 " (cutoff:3.500A) removed outlier: 8.334A pdb=" N ALA J 56 " --> pdb=" O ALA H 53 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N VAL H 55 " --> pdb=" O ALA J 56 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 60 through 66 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 71 Processing sheet with id=AA8, first strand: chain 'D' and resid 46 through 49 removed outlier: 6.812A pdb=" N VAL F 48 " --> pdb=" O GLY D 47 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N VAL D 49 " --> pdb=" O VAL F 48 " (cutoff:3.500A) 45 hydrogen bonds defined for protein. 132 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: 0.93 Time building geometry restraints manager: 1.60 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.28: 710 1.28 - 1.35: 650 1.35 - 1.42: 170 1.42 - 1.49: 871 1.49 - 1.55: 1719 Bond restraints: 4120 Sorted by residual: bond pdb=" CB VAL C 55 " pdb=" CG2 VAL C 55 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.61e+00 bond pdb=" CB VAL I 55 " pdb=" CG2 VAL I 55 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.61e+00 bond pdb=" CB VAL J 55 " pdb=" CG2 VAL J 55 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.59e+00 bond pdb=" CB VAL A 55 " pdb=" CG2 VAL A 55 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.57e+00 bond pdb=" CB VAL B 55 " pdb=" CG2 VAL B 55 " ideal model delta sigma weight residual 1.521 1.459 0.062 3.30e-02 9.18e+02 3.56e+00 ... (remaining 4115 not shown) Histogram of bond angle deviations from ideal: 104.10 - 109.52: 659 109.52 - 114.94: 2039 114.94 - 120.37: 1256 120.37 - 125.79: 1596 125.79 - 131.21: 30 Bond angle restraints: 5580 Sorted by residual: angle pdb=" C VAL C 49 " pdb=" N HIS C 50 " pdb=" CA HIS C 50 " ideal model delta sigma weight residual 122.54 113.32 9.22 1.82e+00 3.02e-01 2.57e+01 angle pdb=" C VAL G 49 " pdb=" N HIS G 50 " pdb=" CA HIS G 50 " ideal model delta sigma weight residual 122.54 113.35 9.19 1.82e+00 3.02e-01 2.55e+01 angle pdb=" C VAL H 49 " pdb=" N HIS H 50 " pdb=" CA HIS H 50 " ideal model delta sigma weight residual 122.54 113.35 9.19 1.82e+00 3.02e-01 2.55e+01 angle pdb=" C VAL B 49 " pdb=" N HIS B 50 " pdb=" CA HIS B 50 " ideal model delta sigma weight residual 122.54 113.36 9.18 1.82e+00 3.02e-01 2.55e+01 angle pdb=" C VAL A 49 " pdb=" N HIS A 50 " pdb=" CA HIS A 50 " ideal model delta sigma weight residual 122.54 113.36 9.18 1.82e+00 3.02e-01 2.54e+01 ... (remaining 5575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 8.65: 1757 8.65 - 17.30: 337 17.30 - 25.96: 196 25.96 - 34.61: 70 34.61 - 43.26: 30 Dihedral angle restraints: 2390 sinusoidal: 770 harmonic: 1620 Sorted by residual: dihedral pdb=" CA GLY H 67 " pdb=" C GLY H 67 " pdb=" N GLY H 68 " pdb=" CA GLY H 68 " ideal model delta harmonic sigma weight residual 180.00 151.15 28.85 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY E 67 " pdb=" C GLY E 67 " pdb=" N GLY E 68 " pdb=" CA GLY E 68 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.33e+01 dihedral pdb=" CA GLY F 67 " pdb=" C GLY F 67 " pdb=" N GLY F 68 " pdb=" CA GLY F 68 " ideal model delta harmonic sigma weight residual 180.00 151.17 28.83 0 5.00e+00 4.00e-02 3.32e+01 ... (remaining 2387 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.077: 527 0.077 - 0.153: 151 0.153 - 0.230: 52 0.230 - 0.306: 0 0.306 - 0.382: 10 Chirality restraints: 740 Sorted by residual: chirality pdb=" CB ILE E 88 " pdb=" CA ILE E 88 " pdb=" CG1 ILE E 88 " pdb=" CG2 ILE E 88 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.66e+00 chirality pdb=" CB ILE A 88 " pdb=" CA ILE A 88 " pdb=" CG1 ILE A 88 " pdb=" CG2 ILE A 88 " both_signs ideal model delta sigma weight residual False 2.64 2.26 0.38 2.00e-01 2.50e+01 3.61e+00 chirality pdb=" CB ILE B 88 " pdb=" CA ILE B 88 " pdb=" CG1 ILE B 88 " pdb=" CG2 ILE B 88 " both_signs ideal model delta sigma weight residual False 2.64 2.27 0.38 2.00e-01 2.50e+01 3.60e+00 ... (remaining 737 not shown) Planarity restraints: 690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE B 88 " 0.009 2.00e-02 2.50e+03 1.74e-02 3.02e+00 pdb=" C ILE B 88 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE B 88 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA B 89 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE H 88 " 0.009 2.00e-02 2.50e+03 1.73e-02 2.98e+00 pdb=" C ILE H 88 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE H 88 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA H 89 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE C 88 " 0.009 2.00e-02 2.50e+03 1.72e-02 2.96e+00 pdb=" C ILE C 88 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE C 88 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA C 89 " 0.010 2.00e-02 2.50e+03 ... (remaining 687 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.73: 427 2.73 - 3.27: 3939 3.27 - 3.81: 6170 3.81 - 4.36: 6849 4.36 - 4.90: 14115 Nonbonded interactions: 31500 Sorted by model distance: nonbonded pdb=" O THR H 72 " pdb=" OG1 THR H 72 " model vdw 2.183 2.440 nonbonded pdb=" O THR B 72 " pdb=" OG1 THR B 72 " model vdw 2.183 2.440 nonbonded pdb=" O THR I 72 " pdb=" OG1 THR I 72 " model vdw 2.183 2.440 nonbonded pdb=" O THR J 72 " pdb=" OG1 THR J 72 " model vdw 2.183 2.440 nonbonded pdb=" O THR E 72 " pdb=" OG1 THR E 72 " model vdw 2.183 2.440 ... (remaining 31495 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' } 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: 0.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.920 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 16.030 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.030 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:2.660 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.400 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7268 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 : 0.012 0.063 4120 Z= 0.784 Angle : 1.453 9.221 5580 Z= 0.826 Chirality : 0.087 0.382 740 Planarity : 0.005 0.017 690 Dihedral : 14.061 43.261 1370 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 28.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 34.48 % Favored : 65.52 % Rotamer: Outliers : 14.88 % Allowed : 11.95 % Favored : 73.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.34 (0.26), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.06 (0.20), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.006 HIS B 50 PHE 0.005 0.002 PHE A 94 TYR 0.011 0.004 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 79 time to evaluate : 0.426 Fit side-chains REVERT: A 62 GLN cc_start: 0.8220 (pt0) cc_final: 0.7984 (pt0) REVERT: A 80 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7287 (mmtm) REVERT: B 57 GLU cc_start: 0.7667 (tt0) cc_final: 0.7362 (tp30) REVERT: B 62 GLN cc_start: 0.7824 (pt0) cc_final: 0.7529 (pt0) REVERT: B 80 LYS cc_start: 0.8473 (OUTLIER) cc_final: 0.7598 (mptt) REVERT: C 57 GLU cc_start: 0.7183 (tt0) cc_final: 0.6793 (tt0) REVERT: C 62 GLN cc_start: 0.8185 (pt0) cc_final: 0.7836 (pt0) REVERT: E 92 THR cc_start: 0.6681 (OUTLIER) cc_final: 0.6268 (p) REVERT: F 92 THR cc_start: 0.6852 (OUTLIER) cc_final: 0.6446 (p) REVERT: G 92 THR cc_start: 0.6609 (OUTLIER) cc_final: 0.6063 (p) REVERT: H 92 THR cc_start: 0.6677 (OUTLIER) cc_final: 0.6059 (p) REVERT: H 96 LYS cc_start: 0.6588 (tppp) cc_final: 0.6123 (mmmt) REVERT: I 92 THR cc_start: 0.6457 (OUTLIER) cc_final: 0.5840 (p) REVERT: J 92 THR cc_start: 0.6243 (OUTLIER) cc_final: 0.5783 (p) outliers start: 61 outliers final: 35 residues processed: 120 average time/residue: 0.1448 time to fit residues: 22.1138 Evaluate side-chains 119 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 76 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 80 LYS Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 72 THR Chi-restraints excluded: chain B residue 74 VAL Chi-restraints excluded: chain B residue 80 LYS Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 72 THR Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 72 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 74 VAL Chi-restraints excluded: chain E residue 92 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 92 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 92 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 74 VAL Chi-restraints excluded: chain H residue 92 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 92 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 92 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 0.0870 chunk 47 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 54 optimal weight: 7.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6966 moved from start: 0.2331 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 4120 Z= 0.161 Angle : 0.883 7.478 5580 Z= 0.457 Chirality : 0.056 0.182 740 Planarity : 0.002 0.008 690 Dihedral : 8.537 27.426 649 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 20.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.41 % Favored : 82.59 % Rotamer: Outliers : 9.27 % Allowed : 17.32 % Favored : 73.41 % 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: -4.83 (0.25), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.67 (0.19), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS B 50 PHE 0.007 0.002 PHE C 94 TYR 0.001 0.000 TYR B 39 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 89 time to evaluate : 0.477 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8122 (pt0) cc_final: 0.7897 (pt0) REVERT: A 80 LYS cc_start: 0.8204 (tptt) cc_final: 0.7395 (pttm) REVERT: B 57 GLU cc_start: 0.7568 (tt0) cc_final: 0.7214 (tp30) REVERT: B 62 GLN cc_start: 0.7885 (pt0) cc_final: 0.7502 (pt0) REVERT: B 80 LYS cc_start: 0.8236 (tptt) cc_final: 0.7267 (pttm) REVERT: C 57 GLU cc_start: 0.7252 (tt0) cc_final: 0.6976 (tt0) REVERT: C 80 LYS cc_start: 0.8259 (tptt) cc_final: 0.8048 (tptt) REVERT: D 52 VAL cc_start: 0.7789 (OUTLIER) cc_final: 0.7483 (t) REVERT: D 80 LYS cc_start: 0.7991 (tptt) cc_final: 0.7245 (tptt) REVERT: E 52 VAL cc_start: 0.7663 (OUTLIER) cc_final: 0.7421 (t) REVERT: E 80 LYS cc_start: 0.7944 (tptt) cc_final: 0.7625 (tptt) REVERT: F 52 VAL cc_start: 0.7810 (OUTLIER) cc_final: 0.7585 (t) REVERT: G 52 VAL cc_start: 0.7857 (OUTLIER) cc_final: 0.7564 (t) REVERT: H 52 VAL cc_start: 0.7698 (OUTLIER) cc_final: 0.7354 (t) REVERT: H 96 LYS cc_start: 0.6574 (tppp) cc_final: 0.5960 (mmmt) REVERT: J 96 LYS cc_start: 0.6097 (tppp) cc_final: 0.5198 (mmmt) outliers start: 38 outliers final: 21 residues processed: 116 average time/residue: 0.1306 time to fit residues: 19.5985 Evaluate side-chains 104 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 78 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 45 optimal weight: 9.9990 chunk 37 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 54 optimal weight: 0.0370 chunk 58 optimal weight: 5.9990 chunk 48 optimal weight: 10.0000 chunk 18 optimal weight: 0.8980 chunk 43 optimal weight: 10.0000 chunk 53 optimal weight: 0.9980 overall best weight: 3.5862 ------------------------------------------------------------------------------- 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: 0.7119 moved from start: 0.2428 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4120 Z= 0.283 Angle : 0.959 6.927 5580 Z= 0.502 Chirality : 0.059 0.160 740 Planarity : 0.003 0.010 690 Dihedral : 9.199 39.202 617 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 22.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.83 % Favored : 75.17 % Rotamer: Outliers : 10.24 % Allowed : 17.32 % Favored : 72.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.94 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.76 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.003 HIS F 50 PHE 0.009 0.002 PHE C 94 TYR 0.003 0.001 TYR J 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 75 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8139 (pt0) cc_final: 0.7856 (pt0) REVERT: A 80 LYS cc_start: 0.8238 (tptt) cc_final: 0.7487 (pttm) REVERT: B 62 GLN cc_start: 0.8049 (pt0) cc_final: 0.7611 (pt0) REVERT: B 80 LYS cc_start: 0.8380 (tptt) cc_final: 0.7299 (pttm) REVERT: C 57 GLU cc_start: 0.7282 (tt0) cc_final: 0.7054 (tt0) REVERT: D 80 LYS cc_start: 0.7832 (tptt) cc_final: 0.6983 (tptt) REVERT: E 80 LYS cc_start: 0.8127 (tptt) cc_final: 0.7773 (tptt) REVERT: H 38 LEU cc_start: 0.6406 (tt) cc_final: 0.6049 (mp) outliers start: 42 outliers final: 38 residues processed: 108 average time/residue: 0.1239 time to fit residues: 17.6902 Evaluate side-chains 111 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 73 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 54 THR Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 10.0000 chunk 28 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 26 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 chunk 54 optimal weight: 10.0000 chunk 57 optimal weight: 7.9990 chunk 51 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 32 optimal weight: 9.9990 overall best weight: 8.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7312 moved from start: 0.2367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.057 4120 Z= 0.599 Angle : 1.288 9.347 5580 Z= 0.688 Chirality : 0.071 0.251 740 Planarity : 0.005 0.019 690 Dihedral : 11.430 55.501 616 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 25.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 26.03 % Favored : 73.97 % Rotamer: Outliers : 11.95 % Allowed : 19.76 % Favored : 68.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.24 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.99 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.011 0.006 HIS F 50 PHE 0.019 0.004 PHE C 94 TYR 0.006 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 71 time to evaluate : 0.481 Fit side-chains REVERT: A 62 GLN cc_start: 0.8191 (pt0) cc_final: 0.7840 (pt0) REVERT: A 80 LYS cc_start: 0.8195 (tptt) cc_final: 0.7616 (pttm) REVERT: B 80 LYS cc_start: 0.8425 (tptt) cc_final: 0.7115 (mmtt) REVERT: C 57 GLU cc_start: 0.7248 (tt0) cc_final: 0.7031 (tt0) REVERT: D 61 GLU cc_start: 0.8251 (OUTLIER) cc_final: 0.8018 (tp30) REVERT: E 80 LYS cc_start: 0.8312 (tptt) cc_final: 0.8055 (tptt) REVERT: H 80 LYS cc_start: 0.7876 (tptt) cc_final: 0.7609 (tptp) outliers start: 49 outliers final: 45 residues processed: 110 average time/residue: 0.1267 time to fit residues: 18.1918 Evaluate side-chains 114 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 68 time to evaluate : 0.400 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 52 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 52 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 10.0000 chunk 43 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 49 optimal weight: 3.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 20.0000 chunk 52 optimal weight: 8.9990 chunk 14 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 11 optimal weight: 8.9990 chunk 34 optimal weight: 0.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- 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: 0.7127 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 4120 Z= 0.263 Angle : 0.963 7.432 5580 Z= 0.502 Chirality : 0.058 0.162 740 Planarity : 0.003 0.009 690 Dihedral : 9.332 48.239 616 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.79 % Favored : 76.21 % Rotamer: Outliers : 12.68 % Allowed : 20.49 % Favored : 66.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.10 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 50 PHE 0.009 0.002 PHE D 94 TYR 0.002 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 73 time to evaluate : 0.419 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8151 (pt0) cc_final: 0.7862 (pt0) REVERT: A 80 LYS cc_start: 0.8028 (tptt) cc_final: 0.7444 (pttm) REVERT: C 57 GLU cc_start: 0.7254 (tt0) cc_final: 0.7012 (tt0) REVERT: D 52 VAL cc_start: 0.8131 (OUTLIER) cc_final: 0.7923 (t) REVERT: E 80 LYS cc_start: 0.8176 (tptt) cc_final: 0.7841 (tptt) REVERT: F 62 GLN cc_start: 0.7719 (OUTLIER) cc_final: 0.7173 (tm-30) outliers start: 52 outliers final: 41 residues processed: 112 average time/residue: 0.1052 time to fit residues: 16.1039 Evaluate side-chains 114 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 71 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 20.0000 chunk 58 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 26 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 0.0030 chunk 30 optimal weight: 8.9990 chunk 55 optimal weight: 6.9990 chunk 6 optimal weight: 0.9990 chunk 33 optimal weight: 9.9990 chunk 42 optimal weight: 5.9990 overall best weight: 3.1998 ------------------------------------------------------------------------------- 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: 0.7117 moved from start: 0.3012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 4120 Z= 0.253 Angle : 0.939 7.118 5580 Z= 0.489 Chirality : 0.058 0.165 740 Planarity : 0.003 0.009 690 Dihedral : 9.109 45.299 616 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 22.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.93 % Favored : 77.07 % Rotamer: Outliers : 12.20 % Allowed : 20.73 % Favored : 67.07 % 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: -4.99 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.002 HIS H 50 PHE 0.008 0.002 PHE C 94 TYR 0.003 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 79 time to evaluate : 0.455 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8225 (pt0) cc_final: 0.7956 (pt0) REVERT: A 80 LYS cc_start: 0.7938 (tptt) cc_final: 0.7357 (pttm) REVERT: C 57 GLU cc_start: 0.7238 (tt0) cc_final: 0.6987 (tt0) REVERT: D 52 VAL cc_start: 0.8172 (OUTLIER) cc_final: 0.7913 (t) REVERT: D 62 GLN cc_start: 0.7709 (OUTLIER) cc_final: 0.7350 (tm-30) REVERT: F 62 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7192 (tm-30) outliers start: 50 outliers final: 42 residues processed: 115 average time/residue: 0.1078 time to fit residues: 16.8120 Evaluate side-chains 122 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 77 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 9.9990 chunk 48 optimal weight: 0.0870 chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 26 optimal weight: 20.0000 chunk 23 optimal weight: 10.0000 chunk 34 optimal weight: 7.9990 chunk 17 optimal weight: 20.0000 chunk 11 optimal weight: 9.9990 chunk 39 optimal weight: 8.9990 overall best weight: 7.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.045 4120 Z= 0.513 Angle : 1.208 8.969 5580 Z= 0.641 Chirality : 0.068 0.193 740 Planarity : 0.004 0.017 690 Dihedral : 10.827 52.758 616 Min Nonbonded Distance : 2.154 Molprobity Statistics. All-atom Clashscore : 25.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 24.14 % Favored : 75.86 % Rotamer: Outliers : 12.20 % Allowed : 22.20 % Favored : 65.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.30 (0.22), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.03 (0.17), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.005 HIS H 50 PHE 0.016 0.003 PHE D 94 TYR 0.006 0.002 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 69 time to evaluate : 0.478 Fit side-chains REVERT: A 80 LYS cc_start: 0.8095 (tptt) cc_final: 0.7520 (pttm) REVERT: C 57 GLU cc_start: 0.7232 (tt0) cc_final: 0.7022 (tt0) REVERT: D 61 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.8008 (tp30) outliers start: 50 outliers final: 48 residues processed: 105 average time/residue: 0.1197 time to fit residues: 16.8689 Evaluate side-chains 118 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 69 time to evaluate : 0.459 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 55 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 74 VAL Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Chi-restraints excluded: chain J residue 74 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.9990 chunk 5 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 55 optimal weight: 0.0040 chunk 50 optimal weight: 7.9990 chunk 53 optimal weight: 4.9990 chunk 32 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 0.9990 overall best weight: 3.0000 ------------------------------------------------------------------------------- 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: 0.7116 moved from start: 0.3137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 4120 Z= 0.244 Angle : 0.945 7.972 5580 Z= 0.492 Chirality : 0.058 0.162 740 Planarity : 0.002 0.009 690 Dihedral : 9.085 47.089 616 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 21.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 21.90 % Favored : 78.10 % Rotamer: Outliers : 11.46 % Allowed : 23.17 % Favored : 65.37 % 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: -4.97 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.78 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS H 50 PHE 0.008 0.002 PHE D 94 TYR 0.002 0.001 TYR H 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 73 time to evaluate : 0.475 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8336 (pt0) cc_final: 0.8093 (pt0) REVERT: A 80 LYS cc_start: 0.7961 (tptt) cc_final: 0.7298 (pttm) REVERT: C 57 GLU cc_start: 0.7226 (tt0) cc_final: 0.6979 (tt0) REVERT: D 52 VAL cc_start: 0.8090 (OUTLIER) cc_final: 0.7880 (t) REVERT: D 62 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7366 (tm-30) REVERT: F 62 GLN cc_start: 0.7680 (OUTLIER) cc_final: 0.7178 (tm-30) outliers start: 47 outliers final: 42 residues processed: 106 average time/residue: 0.1097 time to fit residues: 15.8283 Evaluate side-chains 117 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 72 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 10.0000 chunk 50 optimal weight: 10.0000 chunk 53 optimal weight: 9.9990 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 9.9990 chunk 34 optimal weight: 10.0000 chunk 27 optimal weight: 9.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.0170 chunk 55 optimal weight: 0.8980 chunk 47 optimal weight: 6.9990 overall best weight: 4.1824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7166 moved from start: 0.3099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 4120 Z= 0.314 Angle : 0.989 7.671 5580 Z= 0.517 Chirality : 0.060 0.167 740 Planarity : 0.003 0.011 690 Dihedral : 9.498 47.292 616 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 22.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 23.45 % Favored : 76.55 % Rotamer: Outliers : 11.22 % Allowed : 23.17 % Favored : 65.61 % 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: -4.99 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.80 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.003 HIS H 50 PHE 0.009 0.002 PHE D 94 TYR 0.003 0.001 TYR G 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 71 time to evaluate : 0.340 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8343 (pt0) cc_final: 0.8075 (pt0) REVERT: A 80 LYS cc_start: 0.7970 (tptt) cc_final: 0.7387 (pttm) REVERT: C 57 GLU cc_start: 0.7247 (tt0) cc_final: 0.7010 (tt0) REVERT: D 62 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7374 (tm-30) REVERT: F 62 GLN cc_start: 0.7753 (OUTLIER) cc_final: 0.7209 (tm-30) outliers start: 46 outliers final: 43 residues processed: 105 average time/residue: 0.0901 time to fit residues: 12.8946 Evaluate side-chains 116 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 71 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.9980 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 3.9990 chunk 37 optimal weight: 10.0000 chunk 50 optimal weight: 8.9990 chunk 14 optimal weight: 9.9990 chunk 43 optimal weight: 10.0000 chunk 7 optimal weight: 3.9990 chunk 13 optimal weight: 2.9990 chunk 47 optimal weight: 20.0000 chunk 19 optimal weight: 5.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.3224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4120 Z= 0.276 Angle : 0.947 7.451 5580 Z= 0.493 Chirality : 0.058 0.156 740 Planarity : 0.003 0.010 690 Dihedral : 9.222 47.359 616 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 21.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 22.41 % Favored : 77.59 % Rotamer: Outliers : 11.22 % Allowed : 23.17 % Favored : 65.61 % 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: -4.93 (0.24), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS H 50 PHE 0.009 0.002 PHE D 94 TYR 0.003 0.001 TYR H 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1160 Ramachandran restraints generated. 580 Oldfield, 0 Emsley, 580 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 119 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 73 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: A 62 GLN cc_start: 0.8304 (pt0) cc_final: 0.8052 (pt0) REVERT: A 80 LYS cc_start: 0.7942 (tptt) cc_final: 0.7351 (pttm) REVERT: C 57 GLU cc_start: 0.7230 (tt0) cc_final: 0.6983 (tt0) REVERT: D 52 VAL cc_start: 0.8228 (OUTLIER) cc_final: 0.7972 (t) REVERT: D 62 GLN cc_start: 0.7722 (OUTLIER) cc_final: 0.7365 (tm-30) REVERT: F 62 GLN cc_start: 0.7728 (OUTLIER) cc_final: 0.7199 (tm-30) outliers start: 46 outliers final: 42 residues processed: 106 average time/residue: 0.1095 time to fit residues: 15.8338 Evaluate side-chains 118 residues out of total 420 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 73 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 THR Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 54 THR Chi-restraints excluded: chain A residue 74 VAL Chi-restraints excluded: chain A residue 77 VAL Chi-restraints excluded: chain B residue 44 THR Chi-restraints excluded: chain B residue 48 VAL Chi-restraints excluded: chain B residue 77 VAL Chi-restraints excluded: chain C residue 44 THR Chi-restraints excluded: chain C residue 48 VAL Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 55 VAL Chi-restraints excluded: chain C residue 71 VAL Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 48 VAL Chi-restraints excluded: chain D residue 52 VAL Chi-restraints excluded: chain D residue 62 GLN Chi-restraints excluded: chain E residue 44 THR Chi-restraints excluded: chain E residue 48 VAL Chi-restraints excluded: chain E residue 54 THR Chi-restraints excluded: chain F residue 44 THR Chi-restraints excluded: chain F residue 48 VAL Chi-restraints excluded: chain F residue 52 VAL Chi-restraints excluded: chain F residue 62 GLN Chi-restraints excluded: chain F residue 72 THR Chi-restraints excluded: chain F residue 77 VAL Chi-restraints excluded: chain G residue 44 THR Chi-restraints excluded: chain G residue 48 VAL Chi-restraints excluded: chain G residue 52 VAL Chi-restraints excluded: chain G residue 62 GLN Chi-restraints excluded: chain G residue 72 THR Chi-restraints excluded: chain G residue 77 VAL Chi-restraints excluded: chain H residue 44 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 VAL Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain I residue 44 THR Chi-restraints excluded: chain I residue 48 VAL Chi-restraints excluded: chain I residue 52 VAL Chi-restraints excluded: chain I residue 72 THR Chi-restraints excluded: chain I residue 77 VAL Chi-restraints excluded: chain J residue 44 THR Chi-restraints excluded: chain J residue 48 VAL Chi-restraints excluded: chain J residue 52 VAL Chi-restraints excluded: chain J residue 72 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 9.9990 chunk 6 optimal weight: 10.0000 chunk 8 optimal weight: 9.9990 chunk 41 optimal weight: 20.0000 chunk 2 optimal weight: 10.0000 chunk 34 optimal weight: 8.9990 chunk 54 optimal weight: 0.0670 chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 9.9990 chunk 1 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 overall best weight: 6.6126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 79 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4993 r_free = 0.4993 target = 0.209436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4682 r_free = 0.4682 target = 0.177910 restraints weight = 4617.844| |-----------------------------------------------------------------------------| r_work (start): 0.4676 rms_B_bonded: 2.72 r_work: 0.4559 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4559 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.3009 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.042 4120 Z= 0.460 Angle : 1.138 8.881 5580 Z= 0.601 Chirality : 0.066 0.169 740 Planarity : 0.004 0.015 690 Dihedral : 10.435 51.032 616 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 23.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 25.52 % Favored : 74.48 % Rotamer: Outliers : 11.71 % Allowed : 22.93 % Favored : 65.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.11 (0.23), residues: 580 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.18), residues: 580 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.004 HIS H 50 PHE 0.014 0.003 PHE D 94 TYR 0.005 0.002 TYR H 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1164.86 seconds wall clock time: 23 minutes 2.03 seconds (1382.03 seconds total)