Starting phenix.real_space_refine on Thu Feb 15 22:46:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxr_13104/02_2024/7oxr_13104.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxr_13104/02_2024/7oxr_13104.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxr_13104/02_2024/7oxr_13104.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxr_13104/02_2024/7oxr_13104.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxr_13104/02_2024/7oxr_13104.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7oxr_13104/02_2024/7oxr_13104.pdb" } resolution = 3.3 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 60 5.16 5 C 8670 2.51 5 N 2270 2.21 5 O 2670 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 88": "OD1" <-> "OD2" Residue "A TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 148": "OE1" <-> "OE2" Residue "A ASP 164": "OD1" <-> "OD2" Residue "A GLU 172": "OE1" <-> "OE2" Residue "A ASP 183": "OD1" <-> "OD2" Residue "B ASP 88": "OD1" <-> "OD2" Residue "B TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 148": "OE1" <-> "OE2" Residue "B ASP 164": "OD1" <-> "OD2" Residue "B GLU 172": "OE1" <-> "OE2" Residue "B ASP 183": "OD1" <-> "OD2" Residue "C ASP 88": "OD1" <-> "OD2" Residue "C TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 148": "OE1" <-> "OE2" Residue "C ASP 164": "OD1" <-> "OD2" Residue "C GLU 172": "OE1" <-> "OE2" Residue "C ASP 183": "OD1" <-> "OD2" Residue "D ASP 88": "OD1" <-> "OD2" Residue "D TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 148": "OE1" <-> "OE2" Residue "D ASP 164": "OD1" <-> "OD2" Residue "D GLU 172": "OE1" <-> "OE2" Residue "D ASP 183": "OD1" <-> "OD2" Residue "E ASP 88": "OD1" <-> "OD2" Residue "E TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 148": "OE1" <-> "OE2" Residue "E ASP 164": "OD1" <-> "OD2" Residue "E GLU 172": "OE1" <-> "OE2" Residue "E ASP 183": "OD1" <-> "OD2" Residue "F ASP 88": "OD1" <-> "OD2" Residue "F TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 148": "OE1" <-> "OE2" Residue "F ASP 164": "OD1" <-> "OD2" Residue "F GLU 172": "OE1" <-> "OE2" Residue "F ASP 183": "OD1" <-> "OD2" Residue "G ASP 88": "OD1" <-> "OD2" Residue "G TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 148": "OE1" <-> "OE2" Residue "G ASP 164": "OD1" <-> "OD2" Residue "G GLU 172": "OE1" <-> "OE2" Residue "G ASP 183": "OD1" <-> "OD2" Residue "H ASP 88": "OD1" <-> "OD2" Residue "H TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 148": "OE1" <-> "OE2" Residue "H ASP 164": "OD1" <-> "OD2" Residue "H GLU 172": "OE1" <-> "OE2" Residue "H ASP 183": "OD1" <-> "OD2" Residue "I ASP 88": "OD1" <-> "OD2" Residue "I TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 148": "OE1" <-> "OE2" Residue "I ASP 164": "OD1" <-> "OD2" Residue "I GLU 172": "OE1" <-> "OE2" Residue "I ASP 183": "OD1" <-> "OD2" Residue "J ASP 88": "OD1" <-> "OD2" Residue "J TYR 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 148": "OE1" <-> "OE2" Residue "J ASP 164": "OD1" <-> "OD2" Residue "J GLU 172": "OE1" <-> "OE2" Residue "J ASP 183": "OD1" <-> "OD2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 13670 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "B" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "C" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "D" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "E" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "F" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "G" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "H" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "I" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Chain: "J" Number of atoms: 1367 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1367 Classifications: {'peptide': 170} Link IDs: {'PTRANS': 8, 'TRANS': 161} Chain breaks: 1 Time building chain proxies: 7.58, per 1000 atoms: 0.55 Number of scatterers: 13670 At special positions: 0 Unit cell: (150.592, 157.248, 49.088, 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 60 16.00 O 2670 8.00 N 2270 7.00 C 8670 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=10, symmetry=0 Simple disulfide: pdb=" SG CYS A 113 " - pdb=" SG CYS A 159 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 159 " distance=2.03 Simple disulfide: pdb=" SG CYS C 113 " - pdb=" SG CYS C 159 " distance=2.03 Simple disulfide: pdb=" SG CYS D 113 " - pdb=" SG CYS D 159 " distance=2.03 Simple disulfide: pdb=" SG CYS E 113 " - pdb=" SG CYS E 159 " distance=2.03 Simple disulfide: pdb=" SG CYS F 113 " - pdb=" SG CYS F 159 " distance=2.03 Simple disulfide: pdb=" SG CYS G 113 " - pdb=" SG CYS G 159 " distance=2.03 Simple disulfide: pdb=" SG CYS H 113 " - pdb=" SG CYS H 159 " distance=2.03 Simple disulfide: pdb=" SG CYS I 113 " - pdb=" SG CYS I 159 " distance=2.03 Simple disulfide: pdb=" SG CYS J 113 " - pdb=" SG CYS J 159 " distance=2.03 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: 5.37 Conformation dependent library (CDL) restraints added in 2.6 seconds 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3260 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 10 sheets defined 12.9% alpha, 15.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.06 Creating SS restraints... Processing helix chain 'A' and resid 56 through 58 No H-bonds generated for 'chain 'A' and resid 56 through 58' Processing helix chain 'A' and resid 167 through 175 Processing helix chain 'A' and resid 177 through 186 Processing helix chain 'B' and resid 56 through 58 No H-bonds generated for 'chain 'B' and resid 56 through 58' Processing helix chain 'B' and resid 167 through 175 Processing helix chain 'B' and resid 177 through 186 Processing helix chain 'C' and resid 56 through 58 No H-bonds generated for 'chain 'C' and resid 56 through 58' Processing helix chain 'C' and resid 167 through 175 Processing helix chain 'C' and resid 177 through 186 Processing helix chain 'D' and resid 56 through 58 No H-bonds generated for 'chain 'D' and resid 56 through 58' Processing helix chain 'D' and resid 167 through 175 Processing helix chain 'D' and resid 177 through 186 Processing helix chain 'E' and resid 56 through 58 No H-bonds generated for 'chain 'E' and resid 56 through 58' Processing helix chain 'E' and resid 167 through 175 Processing helix chain 'E' and resid 177 through 186 Processing helix chain 'F' and resid 56 through 58 No H-bonds generated for 'chain 'F' and resid 56 through 58' Processing helix chain 'F' and resid 167 through 175 Processing helix chain 'F' and resid 177 through 186 Processing helix chain 'G' and resid 56 through 58 No H-bonds generated for 'chain 'G' and resid 56 through 58' Processing helix chain 'G' and resid 167 through 175 Processing helix chain 'G' and resid 177 through 186 Processing helix chain 'H' and resid 56 through 58 No H-bonds generated for 'chain 'H' and resid 56 through 58' Processing helix chain 'H' and resid 167 through 175 Processing helix chain 'H' and resid 177 through 186 Processing helix chain 'I' and resid 56 through 58 No H-bonds generated for 'chain 'I' and resid 56 through 58' Processing helix chain 'I' and resid 167 through 175 Processing helix chain 'I' and resid 177 through 186 Processing helix chain 'J' and resid 56 through 58 No H-bonds generated for 'chain 'J' and resid 56 through 58' Processing helix chain 'J' and resid 167 through 175 Processing helix chain 'J' and resid 177 through 186 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 51 through 54 current: chain 'A' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 95 through 98 current: chain 'A' and resid 148 through 160 Processing sheet with id=AA2, first strand: chain 'B' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 51 through 54 current: chain 'B' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 95 through 98 current: chain 'B' and resid 148 through 160 Processing sheet with id=AA3, first strand: chain 'C' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 51 through 54 current: chain 'C' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 95 through 98 current: chain 'C' and resid 148 through 160 Processing sheet with id=AA4, first strand: chain 'D' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 51 through 54 current: chain 'D' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 95 through 98 current: chain 'D' and resid 148 through 160 Processing sheet with id=AA5, first strand: chain 'E' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 51 through 54 current: chain 'E' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 95 through 98 current: chain 'E' and resid 148 through 160 Processing sheet with id=AA6, first strand: chain 'F' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 51 through 54 current: chain 'F' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 95 through 98 current: chain 'F' and resid 148 through 160 Processing sheet with id=AA7, first strand: chain 'G' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 51 through 54 current: chain 'G' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'G' and resid 95 through 98 current: chain 'G' and resid 148 through 160 Processing sheet with id=AA8, first strand: chain 'H' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 51 through 54 current: chain 'H' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'H' and resid 95 through 98 current: chain 'H' and resid 148 through 160 Processing sheet with id=AA9, first strand: chain 'I' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 51 through 54 current: chain 'I' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'I' and resid 95 through 98 current: chain 'I' and resid 148 through 160 Processing sheet with id=AB1, first strand: chain 'J' and resid 51 through 54 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 51 through 54 current: chain 'J' and resid 68 through 77 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 95 through 98 current: chain 'J' and resid 148 through 160 150 hydrogen bonds defined for protein. 420 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: 2.86 Time building geometry restraints manager: 5.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 4510 1.34 - 1.46: 2585 1.46 - 1.57: 6705 1.57 - 1.69: 0 1.69 - 1.80: 100 Bond restraints: 13900 Sorted by residual: bond pdb=" CB PRO J 78 " pdb=" CG PRO J 78 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.63e+00 bond pdb=" CB PRO E 78 " pdb=" CG PRO E 78 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.63e+00 bond pdb=" CB PRO B 78 " pdb=" CG PRO B 78 " ideal model delta sigma weight residual 1.492 1.556 -0.064 5.00e-02 4.00e+02 1.62e+00 bond pdb=" CB PRO I 78 " pdb=" CG PRO I 78 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.60e+00 bond pdb=" CB PRO H 78 " pdb=" CG PRO H 78 " ideal model delta sigma weight residual 1.492 1.555 -0.063 5.00e-02 4.00e+02 1.60e+00 ... (remaining 13895 not shown) Histogram of bond angle deviations from ideal: 101.11 - 107.69: 500 107.69 - 114.26: 8184 114.26 - 120.84: 5448 120.84 - 127.41: 4568 127.41 - 133.99: 110 Bond angle restraints: 18810 Sorted by residual: angle pdb=" CA VAL D 64 " pdb=" C VAL D 64 " pdb=" N GLN D 65 " ideal model delta sigma weight residual 116.60 119.95 -3.35 1.45e+00 4.76e-01 5.35e+00 angle pdb=" CA VAL I 64 " pdb=" C VAL I 64 " pdb=" N GLN I 65 " ideal model delta sigma weight residual 116.60 119.95 -3.35 1.45e+00 4.76e-01 5.32e+00 angle pdb=" CA VAL E 64 " pdb=" C VAL E 64 " pdb=" N GLN E 65 " ideal model delta sigma weight residual 116.60 119.94 -3.34 1.45e+00 4.76e-01 5.32e+00 angle pdb=" CA VAL G 64 " pdb=" C VAL G 64 " pdb=" N GLN G 65 " ideal model delta sigma weight residual 116.60 119.94 -3.34 1.45e+00 4.76e-01 5.31e+00 angle pdb=" CA VAL H 64 " pdb=" C VAL H 64 " pdb=" N GLN H 65 " ideal model delta sigma weight residual 116.60 119.94 -3.34 1.45e+00 4.76e-01 5.31e+00 ... (remaining 18805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.97: 7670 17.97 - 35.94: 732 35.94 - 53.91: 98 53.91 - 71.88: 30 71.88 - 89.86: 60 Dihedral angle restraints: 8590 sinusoidal: 3600 harmonic: 4990 Sorted by residual: dihedral pdb=" CB GLU A 184 " pdb=" CG GLU A 184 " pdb=" CD GLU A 184 " pdb=" OE1 GLU A 184 " ideal model delta sinusoidal sigma weight residual 0.00 79.73 -79.73 1 3.00e+01 1.11e-03 8.77e+00 dihedral pdb=" CB GLU E 184 " pdb=" CG GLU E 184 " pdb=" CD GLU E 184 " pdb=" OE1 GLU E 184 " ideal model delta sinusoidal sigma weight residual 0.00 79.71 -79.71 1 3.00e+01 1.11e-03 8.76e+00 dihedral pdb=" CB GLU D 184 " pdb=" CG GLU D 184 " pdb=" CD GLU D 184 " pdb=" OE1 GLU D 184 " ideal model delta sinusoidal sigma weight residual 0.00 79.69 -79.69 1 3.00e+01 1.11e-03 8.76e+00 ... (remaining 8587 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 1156 0.024 - 0.048: 515 0.048 - 0.071: 271 0.071 - 0.095: 95 0.095 - 0.119: 153 Chirality restraints: 2190 Sorted by residual: chirality pdb=" CA ILE C 219 " pdb=" N ILE C 219 " pdb=" C ILE C 219 " pdb=" CB ILE C 219 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.52e-01 chirality pdb=" CA ILE G 219 " pdb=" N ILE G 219 " pdb=" C ILE G 219 " pdb=" CB ILE G 219 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.47e-01 chirality pdb=" CA ILE B 219 " pdb=" N ILE B 219 " pdb=" C ILE B 219 " pdb=" CB ILE B 219 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.46e-01 ... (remaining 2187 not shown) Planarity restraints: 2420 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER H 167 " -0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO H 168 " 0.130 5.00e-02 4.00e+02 pdb=" CA PRO H 168 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO H 168 " -0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER C 167 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.03e+00 pdb=" N PRO C 168 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO C 168 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO C 168 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER G 167 " 0.049 5.00e-02 4.00e+02 7.51e-02 9.02e+00 pdb=" N PRO G 168 " -0.130 5.00e-02 4.00e+02 pdb=" CA PRO G 168 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO G 168 " 0.041 5.00e-02 4.00e+02 ... (remaining 2417 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 61 2.58 - 3.16: 10589 3.16 - 3.74: 19984 3.74 - 4.32: 29423 4.32 - 4.90: 50855 Nonbonded interactions: 110912 Sorted by model distance: nonbonded pdb=" OH TYR I 182 " pdb=" ND2 ASN J 121 " model vdw 1.998 2.520 nonbonded pdb=" O PRO D 78 " pdb=" NH1 ARG D 98 " model vdw 2.307 2.520 nonbonded pdb=" O PRO I 78 " pdb=" NH1 ARG I 98 " model vdw 2.308 2.520 nonbonded pdb=" O PRO F 78 " pdb=" NH1 ARG F 98 " model vdw 2.308 2.520 nonbonded pdb=" O PRO H 78 " pdb=" NH1 ARG H 98 " model vdw 2.308 2.520 ... (remaining 110907 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: 6.990 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: 0.020 Extract box with map and model: 19.470 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 36.750 Find NCS groups from input model: 0.970 Set up NCS constraints: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 67.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 13900 Z= 0.212 Angle : 0.581 4.882 18810 Z= 0.332 Chirality : 0.043 0.119 2190 Planarity : 0.007 0.075 2420 Dihedral : 16.460 89.855 5300 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 8.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.36 (0.19), residues: 1660 helix: -0.87 (0.38), residues: 150 sheet: -0.76 (0.18), residues: 730 loop : -0.90 (0.20), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP J 186 HIS 0.001 0.001 HIS F 221 PHE 0.007 0.001 PHE E 70 TYR 0.012 0.002 TYR I 182 ARG 0.010 0.001 ARG G 229 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 465 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 465 time to evaluate : 1.701 Fit side-chains REVERT: C 106 ASP cc_start: 0.7820 (m-30) cc_final: 0.7577 (m-30) REVERT: C 108 ASN cc_start: 0.8111 (t0) cc_final: 0.7821 (t0) REVERT: C 148 GLU cc_start: 0.7961 (pt0) cc_final: 0.7758 (pt0) REVERT: E 52 VAL cc_start: 0.9206 (t) cc_final: 0.9000 (t) REVERT: F 103 TYR cc_start: 0.8637 (m-80) cc_final: 0.8140 (m-80) REVERT: F 215 GLN cc_start: 0.7493 (tt0) cc_final: 0.7013 (tt0) REVERT: G 148 GLU cc_start: 0.7976 (pt0) cc_final: 0.7724 (pt0) REVERT: H 103 TYR cc_start: 0.8645 (m-80) cc_final: 0.8137 (m-80) REVERT: H 106 ASP cc_start: 0.7904 (m-30) cc_final: 0.7664 (m-30) REVERT: H 108 ASN cc_start: 0.8133 (t0) cc_final: 0.7838 (t0) REVERT: H 215 GLN cc_start: 0.7508 (tt0) cc_final: 0.7189 (tt0) outliers start: 0 outliers final: 0 residues processed: 465 average time/residue: 0.2954 time to fit residues: 189.6198 Evaluate side-chains 370 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 370 time to evaluate : 1.654 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 143 optimal weight: 2.9990 chunk 128 optimal weight: 0.7980 chunk 71 optimal weight: 3.9990 chunk 44 optimal weight: 0.9990 chunk 86 optimal weight: 1.9990 chunk 68 optimal weight: 2.9990 chunk 133 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 81 optimal weight: 2.9990 chunk 99 optimal weight: 0.9980 chunk 154 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 GLN ** A 215 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 114 GLN B 121 ASN B 173 GLN B 215 GLN C 114 GLN C 215 GLN E 110 GLN E 114 GLN E 215 GLN F 110 GLN F 114 GLN G 114 GLN G 173 GLN G 215 GLN H 114 GLN I 114 GLN I 215 GLN J 215 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8559 moved from start: 0.2692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13900 Z= 0.321 Angle : 0.560 5.776 18810 Z= 0.286 Chirality : 0.046 0.128 2190 Planarity : 0.005 0.070 2420 Dihedral : 4.777 13.898 1800 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.61 % Allowed : 12.98 % Favored : 85.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.20), residues: 1660 helix: -0.02 (0.40), residues: 170 sheet: -0.40 (0.21), residues: 620 loop : -0.83 (0.20), residues: 870 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 186 HIS 0.004 0.002 HIS D 221 PHE 0.011 0.001 PHE I 58 TYR 0.016 0.002 TYR F 182 ARG 0.004 0.001 ARG E 229 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 411 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 385 time to evaluate : 2.272 Fit side-chains revert: symmetry clash REVERT: A 227 LYS cc_start: 0.8622 (ttpt) cc_final: 0.8386 (ttpt) REVERT: C 106 ASP cc_start: 0.7922 (m-30) cc_final: 0.7615 (m-30) REVERT: C 191 ARG cc_start: 0.8046 (mtt-85) cc_final: 0.7835 (mtt-85) REVERT: C 212 GLU cc_start: 0.7960 (tt0) cc_final: 0.7723 (tt0) REVERT: E 227 LYS cc_start: 0.8648 (ttmm) cc_final: 0.8373 (ttpt) REVERT: F 98 ARG cc_start: 0.8817 (tpp-160) cc_final: 0.8572 (tpp-160) REVERT: H 199 GLU cc_start: 0.7912 (tt0) cc_final: 0.7640 (tt0) REVERT: J 130 TYR cc_start: 0.9262 (m-80) cc_final: 0.8971 (m-80) REVERT: J 184 GLU cc_start: 0.7115 (mt-10) cc_final: 0.6876 (mm-30) REVERT: J 193 GLU cc_start: 0.7807 (mt-10) cc_final: 0.7540 (mt-10) outliers start: 26 outliers final: 5 residues processed: 406 average time/residue: 0.3225 time to fit residues: 180.6033 Evaluate side-chains 364 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 359 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 230 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 85 optimal weight: 2.9990 chunk 47 optimal weight: 0.0770 chunk 128 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 154 optimal weight: 1.9990 chunk 167 optimal weight: 1.9990 chunk 137 optimal weight: 1.9990 chunk 153 optimal weight: 0.0970 chunk 52 optimal weight: 1.9990 chunk 124 optimal weight: 2.9990 overall best weight: 0.9740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 173 GLN B 169 GLN B 173 GLN B 215 GLN C 215 GLN D 114 GLN D 215 GLN E 110 GLN E 215 GLN F 110 GLN F 215 GLN G 169 GLN G 215 GLN H 215 GLN I 215 GLN J 100 ASN J 110 GLN J 173 GLN Total number of N/Q/H flips: 19 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8586 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 : 0.005 0.030 13900 Z= 0.302 Angle : 0.511 5.331 18810 Z= 0.259 Chirality : 0.045 0.132 2190 Planarity : 0.005 0.057 2420 Dihedral : 4.635 12.942 1800 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.17 % Allowed : 14.29 % Favored : 83.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.72 (0.21), residues: 1660 helix: 0.44 (0.43), residues: 170 sheet: -0.18 (0.19), residues: 790 loop : -0.93 (0.22), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP C 186 HIS 0.003 0.001 HIS F 152 PHE 0.010 0.001 PHE B 58 TYR 0.012 0.002 TYR A 103 ARG 0.005 0.000 ARG H 229 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 412 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 377 time to evaluate : 1.718 Fit side-chains REVERT: A 102 GLU cc_start: 0.7965 (tt0) cc_final: 0.7709 (tt0) REVERT: C 191 ARG cc_start: 0.8047 (mtt-85) cc_final: 0.7756 (mtt-85) REVERT: C 212 GLU cc_start: 0.7964 (tt0) cc_final: 0.7713 (tt0) REVERT: E 227 LYS cc_start: 0.8642 (ttmm) cc_final: 0.8271 (ttpt) REVERT: H 199 GLU cc_start: 0.7836 (tt0) cc_final: 0.7495 (tt0) REVERT: J 102 GLU cc_start: 0.7868 (tt0) cc_final: 0.7623 (tt0) REVERT: J 193 GLU cc_start: 0.7798 (mt-10) cc_final: 0.7503 (mt-10) outliers start: 35 outliers final: 18 residues processed: 400 average time/residue: 0.3090 time to fit residues: 169.6009 Evaluate side-chains 354 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 336 time to evaluate : 1.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain J residue 211 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 152 optimal weight: 2.9990 chunk 116 optimal weight: 2.9990 chunk 80 optimal weight: 0.6980 chunk 17 optimal weight: 2.9990 chunk 73 optimal weight: 2.9990 chunk 103 optimal weight: 1.9990 chunk 155 optimal weight: 2.9990 chunk 164 optimal weight: 1.9990 chunk 81 optimal weight: 0.9990 chunk 147 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 173 GLN B 173 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN E 215 GLN F 215 GLN H 100 ASN H 215 GLN I 215 GLN J 100 ASN J 110 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8606 moved from start: 0.3627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13900 Z= 0.338 Angle : 0.528 5.438 18810 Z= 0.266 Chirality : 0.046 0.130 2190 Planarity : 0.005 0.054 2420 Dihedral : 4.736 14.112 1800 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.86 % Allowed : 14.47 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.59 (0.21), residues: 1660 helix: 0.50 (0.43), residues: 170 sheet: -0.05 (0.20), residues: 740 loop : -0.87 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 186 HIS 0.004 0.002 HIS E 152 PHE 0.010 0.001 PHE D 58 TYR 0.014 0.002 TYR A 103 ARG 0.005 0.000 ARG G 229 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 387 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 341 time to evaluate : 1.782 Fit side-chains REVERT: A 102 GLU cc_start: 0.8031 (tt0) cc_final: 0.7666 (tp30) REVERT: C 191 ARG cc_start: 0.8062 (mtt-85) cc_final: 0.7731 (mtt-85) REVERT: E 227 LYS cc_start: 0.8672 (ttmm) cc_final: 0.8295 (ttpt) REVERT: H 230 MET cc_start: 0.3665 (tpt) cc_final: 0.3394 (tpt) REVERT: J 102 GLU cc_start: 0.7906 (tt0) cc_final: 0.7516 (tp30) outliers start: 46 outliers final: 16 residues processed: 374 average time/residue: 0.3012 time to fit residues: 155.2997 Evaluate side-chains 351 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 335 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 87 ILE Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 62 ASN Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain C residue 230 MET Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 136 optimal weight: 2.9990 chunk 93 optimal weight: 0.8980 chunk 2 optimal weight: 1.9990 chunk 122 optimal weight: 0.0040 chunk 67 optimal weight: 2.9990 chunk 140 optimal weight: 0.3980 chunk 113 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 147 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 overall best weight: 0.5792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 100 ASN A 173 GLN A 215 GLN B 173 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN F 110 GLN F 215 GLN G 215 GLN H 100 ASN H 215 GLN I 215 GLN J 100 ASN J 110 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.3684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 13900 Z= 0.201 Angle : 0.474 5.151 18810 Z= 0.244 Chirality : 0.044 0.125 2190 Planarity : 0.004 0.050 2420 Dihedral : 4.365 14.833 1800 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 1.99 % Allowed : 16.58 % Favored : 81.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.47 (0.21), residues: 1660 helix: 0.83 (0.44), residues: 170 sheet: 0.04 (0.20), residues: 780 loop : -0.90 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP G 186 HIS 0.002 0.001 HIS E 152 PHE 0.007 0.001 PHE G 58 TYR 0.011 0.001 TYR A 103 ARG 0.007 0.000 ARG F 229 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 346 time to evaluate : 1.716 Fit side-chains REVERT: A 102 GLU cc_start: 0.7969 (tt0) cc_final: 0.7562 (tp30) REVERT: A 103 TYR cc_start: 0.9106 (m-80) cc_final: 0.8827 (m-80) REVERT: B 85 GLN cc_start: 0.8744 (mm-40) cc_final: 0.8532 (mm-40) REVERT: C 98 ARG cc_start: 0.8665 (tpp-160) cc_final: 0.8159 (mmt180) REVERT: C 191 ARG cc_start: 0.8082 (mtt-85) cc_final: 0.7762 (mtt-85) REVERT: E 227 LYS cc_start: 0.8660 (ttmm) cc_final: 0.8278 (ttpt) REVERT: F 98 ARG cc_start: 0.8604 (tpp-160) cc_final: 0.8185 (mmt180) REVERT: G 148 GLU cc_start: 0.8139 (pt0) cc_final: 0.7817 (pt0) REVERT: J 99 ASP cc_start: 0.7284 (t70) cc_final: 0.6917 (t0) REVERT: J 102 GLU cc_start: 0.7950 (tt0) cc_final: 0.7550 (tp30) REVERT: J 212 GLU cc_start: 0.7645 (tt0) cc_final: 0.7433 (tt0) outliers start: 32 outliers final: 18 residues processed: 363 average time/residue: 0.3027 time to fit residues: 150.4383 Evaluate side-chains 367 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 349 time to evaluate : 1.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 215 GLN Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 77 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 77 ILE Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 55 optimal weight: 0.9980 chunk 147 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 96 optimal weight: 0.5980 chunk 40 optimal weight: 2.9990 chunk 164 optimal weight: 0.8980 chunk 136 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 13 optimal weight: 0.6980 chunk 54 optimal weight: 0.0020 chunk 86 optimal weight: 1.9990 overall best weight: 0.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 215 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN F 110 GLN H 100 ASN H 121 ASN H 215 GLN I 121 ASN I 215 GLN J 110 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8581 moved from start: 0.3779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 13900 Z= 0.215 Angle : 0.475 5.250 18810 Z= 0.242 Chirality : 0.044 0.125 2190 Planarity : 0.004 0.048 2420 Dihedral : 4.325 15.483 1800 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.80 % Allowed : 16.89 % Favored : 81.30 % 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: -0.43 (0.22), residues: 1660 helix: 0.84 (0.44), residues: 170 sheet: 0.02 (0.20), residues: 790 loop : -0.82 (0.23), residues: 700 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP C 186 HIS 0.002 0.001 HIS E 152 PHE 0.007 0.001 PHE G 58 TYR 0.010 0.001 TYR H 103 ARG 0.007 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 349 time to evaluate : 1.817 Fit side-chains REVERT: A 102 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7603 (tp30) REVERT: B 85 GLN cc_start: 0.8753 (mm-40) cc_final: 0.8520 (mm-40) REVERT: C 191 ARG cc_start: 0.8084 (mtt-85) cc_final: 0.7775 (mtt-85) REVERT: E 227 LYS cc_start: 0.8638 (ttmm) cc_final: 0.8271 (ttpt) REVERT: J 102 GLU cc_start: 0.7928 (tt0) cc_final: 0.7552 (tp30) REVERT: J 212 GLU cc_start: 0.7695 (tt0) cc_final: 0.7485 (tt0) outliers start: 29 outliers final: 19 residues processed: 363 average time/residue: 0.3143 time to fit residues: 156.8615 Evaluate side-chains 370 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 350 time to evaluate : 1.856 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 230 MET Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 68 THR Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 62 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain I residue 230 MET Chi-restraints excluded: chain J residue 62 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 158 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 93 optimal weight: 0.9990 chunk 120 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 91 optimal weight: 2.9990 chunk 163 optimal weight: 0.0970 chunk 102 optimal weight: 2.9990 chunk 99 optimal weight: 1.9990 chunk 75 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 215 GLN C 100 ASN C 121 ASN C 215 GLN D 121 ASN D 215 GLN E 110 GLN F 110 GLN G 215 GLN H 100 ASN H 121 ASN H 215 GLN I 215 GLN J 110 GLN J 215 GLN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8624 moved from start: 0.3957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.038 13900 Z= 0.412 Angle : 0.575 9.827 18810 Z= 0.283 Chirality : 0.047 0.130 2190 Planarity : 0.005 0.048 2420 Dihedral : 4.754 14.613 1800 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 7.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.42 % Allowed : 16.40 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.43 (0.21), residues: 1660 helix: 0.46 (0.43), residues: 170 sheet: 0.17 (0.20), residues: 740 loop : -0.85 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 186 HIS 0.005 0.002 HIS E 152 PHE 0.011 0.002 PHE I 58 TYR 0.017 0.002 TYR A 103 ARG 0.008 0.001 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 392 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 353 time to evaluate : 1.716 Fit side-chains REVERT: A 102 GLU cc_start: 0.7998 (tt0) cc_final: 0.7622 (tp30) REVERT: E 227 LYS cc_start: 0.8637 (ttmm) cc_final: 0.8258 (ttpt) REVERT: J 102 GLU cc_start: 0.7949 (tt0) cc_final: 0.7554 (tp30) REVERT: J 229 ARG cc_start: 0.8236 (mtm110) cc_final: 0.7991 (mtm110) outliers start: 39 outliers final: 23 residues processed: 375 average time/residue: 0.2967 time to fit residues: 156.9471 Evaluate side-chains 377 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 354 time to evaluate : 1.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain B residue 205 ILE Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 77 ILE Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain F residue 212 GLU Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 77 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 62 ASN Chi-restraints excluded: chain J residue 215 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 65 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 49 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 0.3980 chunk 104 optimal weight: 1.9990 chunk 111 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 128 optimal weight: 0.5980 chunk 149 optimal weight: 3.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 215 GLN C 100 ASN C 215 GLN D 215 GLN E 110 GLN E 121 ASN F 110 GLN G 215 GLN H 100 ASN H 121 ASN H 215 GLN I 215 GLN J 100 ASN J 110 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8580 moved from start: 0.3952 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 13900 Z= 0.192 Angle : 0.495 10.506 18810 Z= 0.245 Chirality : 0.044 0.124 2190 Planarity : 0.004 0.048 2420 Dihedral : 4.376 15.864 1800 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.06 % Allowed : 18.01 % Favored : 80.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.33 (0.22), residues: 1660 helix: 0.85 (0.44), residues: 170 sheet: 0.19 (0.20), residues: 780 loop : -0.88 (0.23), residues: 710 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP E 186 HIS 0.002 0.001 HIS E 152 PHE 0.006 0.001 PHE G 58 TYR 0.013 0.001 TYR A 103 ARG 0.008 0.000 ARG H 191 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 371 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 354 time to evaluate : 1.808 Fit side-chains REVERT: A 102 GLU cc_start: 0.7977 (tt0) cc_final: 0.7742 (tp30) REVERT: A 103 TYR cc_start: 0.9002 (m-80) cc_final: 0.8797 (m-80) REVERT: E 227 LYS cc_start: 0.8629 (ttmm) cc_final: 0.8258 (ttpt) REVERT: G 148 GLU cc_start: 0.8135 (pt0) cc_final: 0.7795 (pt0) REVERT: I 230 MET cc_start: 0.5061 (ppp) cc_final: 0.4761 (pmm) REVERT: J 102 GLU cc_start: 0.7863 (tt0) cc_final: 0.7475 (tp30) outliers start: 17 outliers final: 11 residues processed: 364 average time/residue: 0.3210 time to fit residues: 163.6641 Evaluate side-chains 359 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 348 time to evaluate : 1.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain J residue 77 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 156 optimal weight: 2.9990 chunk 143 optimal weight: 0.5980 chunk 152 optimal weight: 1.9990 chunk 91 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 137 optimal weight: 0.6980 chunk 144 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 161 optimal weight: 2.9990 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 215 GLN C 100 ASN C 121 ASN C 215 GLN D 215 GLN E 110 GLN F 110 GLN G 215 GLN H 100 ASN H 121 ASN H 215 GLN I 215 GLN J 110 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.033 13900 Z= 0.315 Angle : 0.558 11.265 18810 Z= 0.270 Chirality : 0.045 0.127 2190 Planarity : 0.004 0.047 2420 Dihedral : 4.566 16.840 1800 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 1.43 % Allowed : 18.20 % Favored : 80.37 % 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: -0.30 (0.21), residues: 1660 helix: 0.65 (0.44), residues: 170 sheet: 0.26 (0.20), residues: 740 loop : -0.80 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP D 186 HIS 0.004 0.001 HIS H 152 PHE 0.009 0.001 PHE D 58 TYR 0.014 0.002 TYR A 103 ARG 0.009 0.001 ARG A 191 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 378 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 355 time to evaluate : 1.831 Fit side-chains REVERT: A 102 GLU cc_start: 0.8010 (tt0) cc_final: 0.7748 (tp30) REVERT: A 103 TYR cc_start: 0.9029 (m-80) cc_final: 0.8803 (m-80) REVERT: E 227 LYS cc_start: 0.8621 (ttmm) cc_final: 0.8249 (ttpt) REVERT: I 230 MET cc_start: 0.5096 (ppp) cc_final: 0.4762 (pmm) REVERT: J 102 GLU cc_start: 0.7865 (tt0) cc_final: 0.7503 (tp30) outliers start: 23 outliers final: 17 residues processed: 371 average time/residue: 0.2784 time to fit residues: 144.2857 Evaluate side-chains 368 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 351 time to evaluate : 1.565 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 121 ASN Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 98 optimal weight: 1.9990 chunk 76 optimal weight: 0.4980 chunk 112 optimal weight: 1.9990 chunk 169 optimal weight: 0.0770 chunk 155 optimal weight: 2.9990 chunk 134 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 104 optimal weight: 1.9990 chunk 82 optimal weight: 1.9990 chunk 107 optimal weight: 0.9990 chunk 143 optimal weight: 1.9990 overall best weight: 0.8342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 215 GLN C 100 ASN C 121 ASN C 215 GLN D 215 GLN E 110 GLN E 121 ASN F 110 GLN G 215 GLN H 100 ASN H 215 GLN I 215 GLN J 110 GLN Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8599 moved from start: 0.4028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 13900 Z= 0.269 Angle : 0.544 11.621 18810 Z= 0.263 Chirality : 0.045 0.125 2190 Planarity : 0.004 0.047 2420 Dihedral : 4.489 16.497 1800 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 6.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.30 % Allowed : 18.39 % Favored : 80.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.21), residues: 1660 helix: 0.73 (0.44), residues: 170 sheet: 0.27 (0.20), residues: 740 loop : -0.78 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 186 HIS 0.003 0.001 HIS F 152 PHE 0.008 0.001 PHE G 58 TYR 0.013 0.002 TYR E 103 ARG 0.009 0.001 ARG A 191 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3320 Ramachandran restraints generated. 1660 Oldfield, 0 Emsley, 1660 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 367 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 346 time to evaluate : 1.942 Fit side-chains REVERT: A 102 GLU cc_start: 0.8003 (OUTLIER) cc_final: 0.7766 (tp30) REVERT: A 103 TYR cc_start: 0.9037 (m-80) cc_final: 0.8828 (m-80) REVERT: E 227 LYS cc_start: 0.8633 (ttmm) cc_final: 0.8258 (ttpt) REVERT: F 184 GLU cc_start: 0.7618 (mt-10) cc_final: 0.7329 (mm-30) REVERT: G 148 GLU cc_start: 0.8105 (pt0) cc_final: 0.7814 (pt0) REVERT: I 230 MET cc_start: 0.5135 (ppp) cc_final: 0.4798 (pmm) REVERT: J 102 GLU cc_start: 0.7857 (tt0) cc_final: 0.7497 (tp30) outliers start: 21 outliers final: 20 residues processed: 360 average time/residue: 0.2814 time to fit residues: 143.2007 Evaluate side-chains 366 residues out of total 1610 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 345 time to evaluate : 1.746 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 102 GLU Chi-restraints excluded: chain A residue 205 ILE Chi-restraints excluded: chain A residue 211 THR Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 163 THR Chi-restraints excluded: chain C residue 121 ASN Chi-restraints excluded: chain C residue 205 ILE Chi-restraints excluded: chain D residue 77 ILE Chi-restraints excluded: chain E residue 62 ASN Chi-restraints excluded: chain E residue 121 ASN Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 77 ILE Chi-restraints excluded: chain F residue 205 ILE Chi-restraints excluded: chain G residue 68 THR Chi-restraints excluded: chain G residue 205 ILE Chi-restraints excluded: chain H residue 163 THR Chi-restraints excluded: chain H residue 205 ILE Chi-restraints excluded: chain I residue 87 ILE Chi-restraints excluded: chain J residue 77 ILE Chi-restraints excluded: chain J residue 122 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 170 random chunks: chunk 41 optimal weight: 1.9990 chunk 124 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 37 optimal weight: 1.9990 chunk 135 optimal weight: 0.6980 chunk 56 optimal weight: 0.0970 chunk 138 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 118 optimal weight: 0.1980 chunk 7 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 173 GLN B 215 GLN C 100 ASN C 121 ASN C 215 GLN D 215 GLN E 110 GLN E 121 ASN F 110 GLN G 215 GLN H 100 ASN H 121 ASN H 215 GLN I 215 GLN J 110 GLN Total number of N/Q/H flips: 15 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3109 r_free = 0.3109 target = 0.109456 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2748 r_free = 0.2748 target = 0.084539 restraints weight = 15623.728| |-----------------------------------------------------------------------------| r_work (start): 0.2754 rms_B_bonded: 2.03 r_work: 0.2603 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.2428 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.2428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8802 moved from start: 0.4034 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.150 13900 Z= 0.296 Angle : 0.969 59.150 18810 Z= 0.561 Chirality : 0.054 1.102 2190 Planarity : 0.005 0.110 2420 Dihedral : 4.482 16.433 1800 Min Nonbonded Distance : 1.789 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.55 % Allowed : 18.39 % Favored : 80.06 % Cbeta Deviations : 0.12 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.28 (0.21), residues: 1660 helix: 0.74 (0.44), residues: 170 sheet: 0.28 (0.20), residues: 740 loop : -0.81 (0.22), residues: 750 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP A 186 HIS 0.003 0.001 HIS F 152 PHE 0.008 0.001 PHE G 58 TYR 0.011 0.002 TYR E 103 ARG 0.008 0.000 ARG A 191 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3918.18 seconds wall clock time: 72 minutes 13.08 seconds (4333.08 seconds total)