Starting phenix.real_space_refine on Sun Mar 10 19:23:40 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7p_15223/03_2024/8a7p_15223.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7p_15223/03_2024/8a7p_15223.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/8a7p_15223/03_2024/8a7p_15223.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7p_15223/03_2024/8a7p_15223.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7p_15223/03_2024/8a7p_15223.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8a7p_15223/03_2024/8a7p_15223.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= 0.000 sd= 0.001 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 18 5.16 5 C 2760 2.51 5 N 708 2.21 5 O 834 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 12": "NH1" <-> "NH2" Residue "A GLU 16": "OE1" <-> "OE2" Residue "A PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 12": "NH1" <-> "NH2" Residue "B GLU 16": "OE1" <-> "OE2" Residue "B PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 12": "NH1" <-> "NH2" Residue "C GLU 16": "OE1" <-> "OE2" Residue "C PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 12": "NH1" <-> "NH2" Residue "D GLU 16": "OE1" <-> "OE2" Residue "D PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ARG 12": "NH1" <-> "NH2" Residue "E GLU 16": "OE1" <-> "OE2" Residue "E PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 10": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ARG 12": "NH1" <-> "NH2" Residue "F GLU 16": "OE1" <-> "OE2" Residue "F PHE 22": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 26": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 30": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 62": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4320 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "B" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "C" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "D" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "E" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Chain: "F" Number of atoms: 720 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 720 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 4, 'TRANS': 82} Time building chain proxies: 2.75, per 1000 atoms: 0.64 Number of scatterers: 4320 At special positions: 0 Unit cell: (155.21, 104.58, 33.2, 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 18 16.00 O 834 8.00 N 708 7.00 C 2760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 25 " - pdb=" SG CYS A 80 " distance=2.03 Simple disulfide: pdb=" SG CYS B 25 " - pdb=" SG CYS B 80 " distance=2.03 Simple disulfide: pdb=" SG CYS C 25 " - pdb=" SG CYS C 80 " distance=2.03 Simple disulfide: pdb=" SG CYS D 25 " - pdb=" SG CYS D 80 " distance=2.03 Simple disulfide: pdb=" SG CYS E 25 " - pdb=" SG CYS E 80 " distance=2.03 Simple disulfide: pdb=" SG CYS F 25 " - pdb=" SG CYS F 80 " 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: 1.62 Conformation dependent library (CDL) restraints added in 747.4 milliseconds 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1008 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 24 sheets defined 0.0% alpha, 46.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 12 removed outlier: 6.605A pdb=" N GLN A 8 " --> pdb=" O VAL C 9 " (cutoff:3.500A) removed outlier: 7.856A pdb=" N SER C 11 " --> pdb=" O GLN A 8 " (cutoff:3.500A) removed outlier: 6.107A pdb=" N TYR A 10 " --> pdb=" O SER C 11 " (cutoff:3.500A) removed outlier: 6.614A pdb=" N GLN C 8 " --> pdb=" O VAL E 9 " (cutoff:3.500A) removed outlier: 7.859A pdb=" N SER E 11 " --> pdb=" O GLN C 8 " (cutoff:3.500A) removed outlier: 6.088A pdb=" N TYR C 10 " --> pdb=" O SER E 11 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 15 through 17 Processing sheet with id=AA3, first strand: chain 'A' and resid 20 through 22 removed outlier: 6.956A pdb=" N ASN C 21 " --> pdb=" O SER A 20 " (cutoff:3.500A) removed outlier: 6.749A pdb=" N ASN E 21 " --> pdb=" O SER C 20 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 33 through 39 removed outlier: 6.908A pdb=" N ASP C 34 " --> pdb=" O SER A 33 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ASP E 34 " --> pdb=" O SER C 33 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 42 through 49 removed outlier: 6.771A pdb=" N ILE C 46 " --> pdb=" O ARG A 45 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N GLU A 47 " --> pdb=" O ILE C 46 " (cutoff:3.500A) removed outlier: 6.808A pdb=" N ILE E 46 " --> pdb=" O ARG C 45 " (cutoff:3.500A) removed outlier: 6.936A pdb=" N GLU C 47 " --> pdb=" O ILE E 46 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 52 through 53 removed outlier: 6.818A pdb=" N SER A 52 " --> pdb=" O ASP C 53 " (cutoff:3.500A) removed outlier: 6.723A pdb=" N SER C 52 " --> pdb=" O ASP E 53 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 59 through 66 removed outlier: 7.094A pdb=" N TYR C 63 " --> pdb=" O PHE A 62 " (cutoff:3.500A) removed outlier: 7.216A pdb=" N LEU A 64 " --> pdb=" O TYR C 63 " (cutoff:3.500A) removed outlier: 7.054A pdb=" N LEU C 65 " --> pdb=" O LEU A 64 " (cutoff:3.500A) removed outlier: 7.133A pdb=" N TYR A 66 " --> pdb=" O LEU C 65 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N TYR E 63 " --> pdb=" O PHE C 62 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N LEU C 64 " --> pdb=" O TYR E 63 " (cutoff:3.500A) removed outlier: 6.868A pdb=" N LEU E 65 " --> pdb=" O LEU C 64 " (cutoff:3.500A) removed outlier: 6.961A pdb=" N TYR C 66 " --> pdb=" O LEU E 65 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 69 through 70 Processing sheet with id=AA9, first strand: chain 'A' and resid 73 through 74 Processing sheet with id=AB1, first strand: chain 'A' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'A' and resid 81 through 83 Processing sheet with id=AB3, first strand: chain 'A' and resid 86 through 88 Processing sheet with id=AB4, first strand: chain 'B' and resid 7 through 12 removed outlier: 6.450A pdb=" N GLN B 8 " --> pdb=" O VAL D 9 " (cutoff:3.500A) removed outlier: 7.708A pdb=" N SER D 11 " --> pdb=" O GLN B 8 " (cutoff:3.500A) removed outlier: 5.940A pdb=" N TYR B 10 " --> pdb=" O SER D 11 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 15 through 17 Processing sheet with id=AB6, first strand: chain 'B' and resid 20 through 22 removed outlier: 6.832A pdb=" N ASN D 21 " --> pdb=" O SER B 20 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ASN F 21 " --> pdb=" O SER D 20 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'B' and resid 33 through 39 removed outlier: 6.842A pdb=" N ASP D 34 " --> pdb=" O SER B 33 " (cutoff:3.500A) removed outlier: 6.839A pdb=" N ASP F 34 " --> pdb=" O SER D 33 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'B' and resid 42 through 53 removed outlier: 6.831A pdb=" N ILE D 46 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU B 47 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER D 52 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP B 53 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N ILE F 46 " --> pdb=" O ARG D 45 " (cutoff:3.500A) removed outlier: 6.915A pdb=" N GLU D 47 " --> pdb=" O ILE F 46 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'B' and resid 42 through 53 removed outlier: 6.831A pdb=" N ILE D 46 " --> pdb=" O ARG B 45 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N GLU B 47 " --> pdb=" O ILE D 46 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N SER D 52 " --> pdb=" O HIS B 51 " (cutoff:3.500A) removed outlier: 7.017A pdb=" N ASP B 53 " --> pdb=" O SER D 52 " (cutoff:3.500A) removed outlier: 8.626A pdb=" N ASP F 53 " --> pdb=" O GLU D 50 " (cutoff:3.500A) removed outlier: 6.651A pdb=" N SER D 52 " --> pdb=" O ASP F 53 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'B' and resid 59 through 66 removed outlier: 7.010A pdb=" N TYR D 63 " --> pdb=" O PHE B 62 " (cutoff:3.500A) removed outlier: 7.126A pdb=" N LEU B 64 " --> pdb=" O TYR D 63 " (cutoff:3.500A) removed outlier: 6.978A pdb=" N LEU D 65 " --> pdb=" O LEU B 64 " (cutoff:3.500A) removed outlier: 7.055A pdb=" N TYR B 66 " --> pdb=" O LEU D 65 " (cutoff:3.500A) removed outlier: 6.993A pdb=" N TYR F 63 " --> pdb=" O PHE D 62 " (cutoff:3.500A) removed outlier: 7.083A pdb=" N LEU D 64 " --> pdb=" O TYR F 63 " (cutoff:3.500A) removed outlier: 6.923A pdb=" N LEU F 65 " --> pdb=" O LEU D 64 " (cutoff:3.500A) removed outlier: 7.007A pdb=" N TYR D 66 " --> pdb=" O LEU F 65 " (cutoff:3.500A) Processing sheet with id=AC2, first strand: chain 'B' and resid 69 through 70 Processing sheet with id=AC3, first strand: chain 'B' and resid 73 through 74 Processing sheet with id=AC4, first strand: chain 'B' and resid 77 through 78 Processing sheet with id=AC5, first strand: chain 'B' and resid 81 through 83 Processing sheet with id=AC6, first strand: chain 'B' and resid 86 through 88 removed outlier: 6.304A pdb=" N LEU D 87 " --> pdb=" O SER F 88 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 300 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: 1.01 Time building geometry restraints manager: 1.76 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: 1380 1.34 - 1.46: 988 1.46 - 1.58: 2048 1.58 - 1.69: 0 1.69 - 1.81: 24 Bond restraints: 4440 Sorted by residual: bond pdb=" CA ALA F 79 " pdb=" C ALA F 79 " ideal model delta sigma weight residual 1.523 1.534 -0.011 1.61e-02 3.86e+03 4.73e-01 bond pdb=" CA ALA B 79 " pdb=" C ALA B 79 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.61e-02 3.86e+03 4.09e-01 bond pdb=" CA ALA A 79 " pdb=" C ALA A 79 " ideal model delta sigma weight residual 1.523 1.533 -0.010 1.61e-02 3.86e+03 3.91e-01 bond pdb=" CA ALA E 79 " pdb=" C ALA E 79 " ideal model delta sigma weight residual 1.523 1.532 -0.010 1.61e-02 3.86e+03 3.66e-01 bond pdb=" CA ALA C 79 " pdb=" C ALA C 79 " ideal model delta sigma weight residual 1.523 1.532 -0.009 1.61e-02 3.86e+03 3.44e-01 ... (remaining 4435 not shown) Histogram of bond angle deviations from ideal: 100.73 - 107.37: 171 107.37 - 114.02: 2429 114.02 - 120.66: 1718 120.66 - 127.31: 1640 127.31 - 133.95: 54 Bond angle restraints: 6012 Sorted by residual: angle pdb=" C PRO C 14 " pdb=" N ALA C 15 " pdb=" CA ALA C 15 " ideal model delta sigma weight residual 121.94 118.18 3.76 1.76e+00 3.23e-01 4.58e+00 angle pdb=" C PRO E 14 " pdb=" N ALA E 15 " pdb=" CA ALA E 15 " ideal model delta sigma weight residual 121.94 118.19 3.75 1.76e+00 3.23e-01 4.55e+00 angle pdb=" C PRO B 14 " pdb=" N ALA B 15 " pdb=" CA ALA B 15 " ideal model delta sigma weight residual 121.94 118.23 3.71 1.76e+00 3.23e-01 4.44e+00 angle pdb=" C PRO A 14 " pdb=" N ALA A 15 " pdb=" CA ALA A 15 " ideal model delta sigma weight residual 121.94 118.24 3.70 1.76e+00 3.23e-01 4.41e+00 angle pdb=" C PRO D 14 " pdb=" N ALA D 15 " pdb=" CA ALA D 15 " ideal model delta sigma weight residual 121.94 118.26 3.68 1.76e+00 3.23e-01 4.38e+00 ... (remaining 6007 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.54: 2461 13.54 - 27.07: 135 27.07 - 40.61: 32 40.61 - 54.15: 15 54.15 - 67.69: 9 Dihedral angle restraints: 2652 sinusoidal: 1092 harmonic: 1560 Sorted by residual: dihedral pdb=" N LYS E 58 " pdb=" CA LYS E 58 " pdb=" CB LYS E 58 " pdb=" CG LYS E 58 " ideal model delta sinusoidal sigma weight residual -60.00 -103.10 43.10 3 1.50e+01 4.44e-03 7.74e+00 dihedral pdb=" N LYS C 58 " pdb=" CA LYS C 58 " pdb=" CB LYS C 58 " pdb=" CG LYS C 58 " ideal model delta sinusoidal sigma weight residual -60.00 -103.08 43.08 3 1.50e+01 4.44e-03 7.74e+00 dihedral pdb=" N LYS A 58 " pdb=" CA LYS A 58 " pdb=" CB LYS A 58 " pdb=" CG LYS A 58 " ideal model delta sinusoidal sigma weight residual -60.00 -103.04 43.04 3 1.50e+01 4.44e-03 7.73e+00 ... (remaining 2649 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 366 0.028 - 0.056: 174 0.056 - 0.085: 30 0.085 - 0.113: 35 0.113 - 0.141: 25 Chirality restraints: 630 Sorted by residual: chirality pdb=" CA PRO D 14 " pdb=" N PRO D 14 " pdb=" C PRO D 14 " pdb=" CB PRO D 14 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.98e-01 chirality pdb=" CA PRO E 14 " pdb=" N PRO E 14 " pdb=" C PRO E 14 " pdb=" CB PRO E 14 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 chirality pdb=" CA PRO A 14 " pdb=" N PRO A 14 " pdb=" C PRO A 14 " pdb=" CB PRO A 14 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.95e-01 ... (remaining 627 not shown) Planarity restraints: 774 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS B 13 " 0.033 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO B 14 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO B 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 14 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS D 13 " 0.032 5.00e-02 4.00e+02 4.92e-02 3.87e+00 pdb=" N PRO D 14 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO D 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO D 14 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS F 13 " 0.032 5.00e-02 4.00e+02 4.88e-02 3.82e+00 pdb=" N PRO F 14 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO F 14 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO F 14 " 0.027 5.00e-02 4.00e+02 ... (remaining 771 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1137 2.83 - 3.35: 3283 3.35 - 3.87: 7097 3.87 - 4.38: 7181 4.38 - 4.90: 14250 Nonbonded interactions: 32948 Sorted by model distance: nonbonded pdb=" O LYS C 58 " pdb=" N LYS E 58 " model vdw 2.313 2.520 nonbonded pdb=" O LYS B 58 " pdb=" N LYS D 58 " model vdw 2.338 2.520 nonbonded pdb=" O LYS A 58 " pdb=" N LYS C 58 " model vdw 2.346 2.520 nonbonded pdb=" O LYS D 58 " pdb=" N LYS F 58 " model vdw 2.375 2.520 nonbonded pdb=" OE1 GLU C 47 " pdb=" NH1 ARG D 45 " model vdw 2.546 2.520 ... (remaining 32943 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.940 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: 12.620 Check model and map are aligned: 0.060 Set scattering table: 0.060 Process input model: 15.900 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7417 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 : 0.002 0.014 4440 Z= 0.141 Angle : 0.545 3.765 6012 Z= 0.326 Chirality : 0.044 0.141 630 Planarity : 0.005 0.049 774 Dihedral : 10.478 67.686 1626 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 1.83 % Allowed : 1.22 % Favored : 96.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.55 (0.30), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.70 (0.23), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP B 60 HIS 0.003 0.001 HIS F 31 PHE 0.012 0.002 PHE A 22 TYR 0.006 0.001 TYR D 63 ARG 0.002 0.000 ARG E 12 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 0.570 Fit side-chains REVERT: B 89 GLN cc_start: 0.6643 (tt0) cc_final: 0.6005 (mt0) REVERT: D 89 GLN cc_start: 0.6838 (tt0) cc_final: 0.6042 (mt0) REVERT: E 53 ASP cc_start: 0.7896 (t0) cc_final: 0.7665 (t0) REVERT: F 89 GLN cc_start: 0.6597 (tt0) cc_final: 0.6134 (mt0) outliers start: 9 outliers final: 3 residues processed: 126 average time/residue: 0.1876 time to fit residues: 28.7954 Evaluate side-chains 67 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 64 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 24 optimal weight: 10.0000 chunk 19 optimal weight: 9.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 5.9990 chunk 28 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 HIS A 84 HIS B 31 HIS C 31 HIS C 84 HIS D 84 HIS E 31 HIS E 84 HIS E 89 GLN F 31 HIS Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4440 Z= 0.278 Angle : 0.681 5.455 6012 Z= 0.384 Chirality : 0.050 0.153 630 Planarity : 0.005 0.051 774 Dihedral : 5.783 29.271 573 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer: Outliers : 2.24 % Allowed : 11.59 % Favored : 86.18 % 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: -3.45 (0.28), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.62 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 60 HIS 0.005 0.001 HIS B 31 PHE 0.021 0.003 PHE D 22 TYR 0.016 0.003 TYR D 26 ARG 0.002 0.000 ARG A 45 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 78 time to evaluate : 0.541 Fit side-chains REVERT: A 36 GLU cc_start: 0.7980 (tt0) cc_final: 0.7656 (tt0) REVERT: A 38 ASP cc_start: 0.8567 (p0) cc_final: 0.8099 (p0) REVERT: A 40 LEU cc_start: 0.9339 (tp) cc_final: 0.9038 (tt) REVERT: B 20 SER cc_start: 0.9011 (p) cc_final: 0.8770 (p) REVERT: B 45 ARG cc_start: 0.7939 (OUTLIER) cc_final: 0.7702 (mtm-85) REVERT: B 89 GLN cc_start: 0.6919 (tt0) cc_final: 0.6353 (mt0) REVERT: D 89 GLN cc_start: 0.7071 (tt0) cc_final: 0.6401 (mt0) REVERT: E 74 GLU cc_start: 0.8008 (pm20) cc_final: 0.7777 (pm20) REVERT: F 89 GLN cc_start: 0.6462 (tt0) cc_final: 0.6118 (mt0) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.1402 time to fit residues: 16.2445 Evaluate side-chains 80 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.534 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 28 SER Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.0970 chunk 13 optimal weight: 7.9990 chunk 36 optimal weight: 0.0670 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 43 optimal weight: 0.1980 chunk 47 optimal weight: 5.9990 chunk 38 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 35 optimal weight: 6.9990 chunk 32 optimal weight: 0.0470 overall best weight: 0.4816 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 51 HIS D 31 HIS E 13 HIS E 42 ASN E 51 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.3546 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4440 Z= 0.120 Angle : 0.539 6.411 6012 Z= 0.294 Chirality : 0.045 0.129 630 Planarity : 0.004 0.044 774 Dihedral : 5.159 22.433 573 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.10 % Favored : 94.90 % Rotamer: Outliers : 2.64 % Allowed : 14.23 % Favored : 83.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.41 (0.29), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.59 (0.22), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 60 HIS 0.002 0.000 HIS D 31 PHE 0.019 0.002 PHE C 22 TYR 0.015 0.001 TYR E 67 ARG 0.001 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 73 time to evaluate : 0.581 Fit side-chains REVERT: A 34 ASP cc_start: 0.8262 (m-30) cc_final: 0.8056 (m-30) REVERT: A 38 ASP cc_start: 0.8197 (p0) cc_final: 0.7944 (p0) REVERT: B 45 ARG cc_start: 0.7940 (OUTLIER) cc_final: 0.7578 (mtm-85) REVERT: B 89 GLN cc_start: 0.6766 (tt0) cc_final: 0.6166 (mt0) REVERT: E 16 GLU cc_start: 0.7517 (mp0) cc_final: 0.7277 (mm-30) REVERT: E 74 GLU cc_start: 0.7906 (pm20) cc_final: 0.7670 (pm20) REVERT: F 89 GLN cc_start: 0.6396 (tt0) cc_final: 0.6080 (mt0) outliers start: 13 outliers final: 11 residues processed: 80 average time/residue: 0.1487 time to fit residues: 15.4343 Evaluate side-chains 78 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 66 time to evaluate : 0.533 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 57 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 7.9990 chunk 4 optimal weight: 2.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 43 optimal weight: 7.9990 chunk 46 optimal weight: 6.9990 chunk 41 optimal weight: 10.0000 chunk 12 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 13 HIS C 13 HIS F 24 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7803 moved from start: 0.4266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 4440 Z= 0.409 Angle : 0.722 6.240 6012 Z= 0.412 Chirality : 0.053 0.153 630 Planarity : 0.005 0.045 774 Dihedral : 6.190 31.040 573 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 10.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.86 % Favored : 93.14 % Rotamer: Outliers : 4.47 % Allowed : 14.02 % Favored : 81.50 % 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: -3.49 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.65 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP B 60 HIS 0.004 0.001 HIS B 31 PHE 0.023 0.003 PHE A 30 TYR 0.023 0.003 TYR F 26 ARG 0.002 0.000 ARG D 45 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 74 time to evaluate : 0.547 Fit side-chains REVERT: A 36 GLU cc_start: 0.8012 (tt0) cc_final: 0.7759 (tt0) REVERT: B 45 ARG cc_start: 0.7909 (OUTLIER) cc_final: 0.7639 (mtm-85) REVERT: D 45 ARG cc_start: 0.7807 (OUTLIER) cc_final: 0.7521 (ttm170) REVERT: E 42 ASN cc_start: 0.8911 (m110) cc_final: 0.8557 (m110) REVERT: F 89 GLN cc_start: 0.6466 (tt0) cc_final: 0.6009 (mt0) outliers start: 22 outliers final: 18 residues processed: 86 average time/residue: 0.1458 time to fit residues: 16.3717 Evaluate side-chains 89 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 45 ARG Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 55 SER Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 40 LEU Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 4.9990 chunk 19 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 23 optimal weight: 7.9990 chunk 41 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 9 optimal weight: 0.0970 chunk 27 optimal weight: 0.8980 overall best weight: 3.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7769 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4440 Z= 0.259 Angle : 0.644 6.238 6012 Z= 0.361 Chirality : 0.049 0.141 630 Planarity : 0.004 0.043 774 Dihedral : 5.952 27.780 573 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.86 % Allowed : 15.65 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.76 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP D 60 HIS 0.003 0.001 HIS B 31 PHE 0.020 0.003 PHE D 22 TYR 0.015 0.002 TYR F 26 ARG 0.001 0.000 ARG C 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.551 Fit side-chains REVERT: B 45 ARG cc_start: 0.7963 (OUTLIER) cc_final: 0.7743 (mtm-85) REVERT: D 6 MET cc_start: 0.6285 (ttm) cc_final: 0.5982 (ttm) REVERT: E 42 ASN cc_start: 0.8825 (m110) cc_final: 0.8535 (m110) REVERT: F 89 GLN cc_start: 0.6475 (tt0) cc_final: 0.5949 (mt0) outliers start: 19 outliers final: 15 residues processed: 83 average time/residue: 0.1676 time to fit residues: 17.7761 Evaluate side-chains 87 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 71 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 10.0000 chunk 46 optimal weight: 20.0000 chunk 38 optimal weight: 9.9990 chunk 21 optimal weight: 10.0000 chunk 3 optimal weight: 10.0000 chunk 15 optimal weight: 9.9990 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 7.9990 chunk 5 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 0.0010 overall best weight: 5.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 51 HIS B 51 HIS ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 51 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7854 moved from start: 0.4852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4440 Z= 0.390 Angle : 0.728 6.662 6012 Z= 0.414 Chirality : 0.053 0.152 630 Planarity : 0.005 0.045 774 Dihedral : 6.446 31.626 573 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.82 % Favored : 91.18 % Rotamer: Outliers : 4.47 % Allowed : 15.24 % Favored : 80.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.77 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 60 HIS 0.004 0.001 HIS B 31 PHE 0.022 0.003 PHE D 22 TYR 0.021 0.003 TYR F 26 ARG 0.013 0.001 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 75 time to evaluate : 0.540 Fit side-chains REVERT: A 34 ASP cc_start: 0.8162 (m-30) cc_final: 0.7623 (t0) REVERT: A 40 LEU cc_start: 0.9429 (OUTLIER) cc_final: 0.9200 (tt) REVERT: B 45 ARG cc_start: 0.7951 (OUTLIER) cc_final: 0.7662 (mtm-85) REVERT: B 81 ARG cc_start: 0.7679 (ttm110) cc_final: 0.7355 (mtm180) REVERT: C 75 LYS cc_start: 0.7886 (mtmt) cc_final: 0.7208 (tttp) REVERT: E 42 ASN cc_start: 0.8860 (m110) cc_final: 0.8398 (m110) REVERT: F 89 GLN cc_start: 0.6440 (tt0) cc_final: 0.5719 (mt0) outliers start: 22 outliers final: 18 residues processed: 87 average time/residue: 0.1478 time to fit residues: 16.5952 Evaluate side-chains 92 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.490 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 34 ASP Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Chi-restraints excluded: chain F residue 55 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 3.9990 chunk 39 optimal weight: 10.0000 chunk 25 optimal weight: 0.8980 chunk 46 optimal weight: 8.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4440 Z= 0.174 Angle : 0.616 7.129 6012 Z= 0.338 Chirality : 0.048 0.144 630 Planarity : 0.004 0.038 774 Dihedral : 5.711 24.570 573 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.66 % Allowed : 17.48 % Favored : 78.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.76 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.85 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 60 HIS 0.002 0.000 HIS D 31 PHE 0.022 0.002 PHE D 22 TYR 0.010 0.001 TYR A 67 ARG 0.007 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 80 time to evaluate : 0.540 Fit side-chains REVERT: A 40 LEU cc_start: 0.9380 (OUTLIER) cc_final: 0.9142 (tt) REVERT: B 45 ARG cc_start: 0.7922 (OUTLIER) cc_final: 0.7630 (mtm-85) REVERT: B 81 ARG cc_start: 0.7639 (ttm110) cc_final: 0.7373 (mtm180) REVERT: C 40 LEU cc_start: 0.9313 (OUTLIER) cc_final: 0.9046 (tt) REVERT: E 42 ASN cc_start: 0.8694 (m110) cc_final: 0.8428 (m-40) REVERT: F 89 GLN cc_start: 0.6475 (tt0) cc_final: 0.5815 (mt0) outliers start: 18 outliers final: 12 residues processed: 89 average time/residue: 0.1540 time to fit residues: 17.7331 Evaluate side-chains 88 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 8.9990 chunk 31 optimal weight: 5.9990 chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 36 optimal weight: 9.9990 chunk 42 optimal weight: 1.9990 chunk 44 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 5.9990 chunk 25 optimal weight: 9.9990 chunk 18 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7793 moved from start: 0.4931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4440 Z= 0.225 Angle : 0.637 7.129 6012 Z= 0.354 Chirality : 0.049 0.138 630 Planarity : 0.004 0.036 774 Dihedral : 5.819 26.918 573 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.63 % Favored : 91.37 % Rotamer: Outliers : 3.46 % Allowed : 17.07 % Favored : 79.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.78 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.87 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP F 60 HIS 0.003 0.001 HIS D 31 PHE 0.029 0.003 PHE E 70 TYR 0.013 0.002 TYR D 63 ARG 0.007 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.519 Fit side-chains REVERT: A 24 ASN cc_start: 0.8279 (m-40) cc_final: 0.8006 (m-40) REVERT: A 40 LEU cc_start: 0.9373 (OUTLIER) cc_final: 0.9138 (tt) REVERT: B 45 ARG cc_start: 0.7894 (OUTLIER) cc_final: 0.7651 (mtm-85) REVERT: B 81 ARG cc_start: 0.7638 (ttm110) cc_final: 0.7362 (mtm180) REVERT: C 40 LEU cc_start: 0.9289 (OUTLIER) cc_final: 0.8988 (tt) REVERT: E 16 GLU cc_start: 0.7343 (mp0) cc_final: 0.7066 (mp0) REVERT: E 42 ASN cc_start: 0.8717 (m110) cc_final: 0.8424 (m110) REVERT: F 89 GLN cc_start: 0.6509 (tt0) cc_final: 0.5727 (mt0) outliers start: 17 outliers final: 14 residues processed: 84 average time/residue: 0.1489 time to fit residues: 16.1084 Evaluate side-chains 90 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 73 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 8.9990 chunk 13 optimal weight: 5.9990 chunk 38 optimal weight: 3.9990 chunk 40 optimal weight: 9.9990 chunk 42 optimal weight: 6.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 21 optimal weight: 10.0000 chunk 31 optimal weight: 10.0000 chunk 47 optimal weight: 9.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 24 ASN ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.5212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 4440 Z= 0.405 Angle : 0.743 6.899 6012 Z= 0.422 Chirality : 0.054 0.191 630 Planarity : 0.005 0.038 774 Dihedral : 6.372 31.766 573 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 4.07 % Allowed : 16.26 % Favored : 79.67 % 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: -3.90 (0.26), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (0.20), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 60 HIS 0.005 0.001 HIS D 31 PHE 0.030 0.003 PHE C 22 TYR 0.020 0.003 TYR F 26 ARG 0.006 0.000 ARG B 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 73 time to evaluate : 0.523 Fit side-chains REVERT: A 24 ASN cc_start: 0.8540 (m110) cc_final: 0.8248 (m-40) REVERT: A 34 ASP cc_start: 0.8169 (m-30) cc_final: 0.7627 (t0) REVERT: A 40 LEU cc_start: 0.9401 (OUTLIER) cc_final: 0.9188 (tt) REVERT: B 81 ARG cc_start: 0.7682 (ttm110) cc_final: 0.7363 (mtm180) REVERT: C 16 GLU cc_start: 0.7515 (mp0) cc_final: 0.6325 (tp30) REVERT: C 40 LEU cc_start: 0.9296 (OUTLIER) cc_final: 0.8982 (tt) REVERT: F 89 GLN cc_start: 0.6356 (tt0) cc_final: 0.5662 (mt0) outliers start: 20 outliers final: 16 residues processed: 83 average time/residue: 0.1321 time to fit residues: 14.5654 Evaluate side-chains 89 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 71 time to evaluate : 0.525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 55 SER Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 33 SER Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 55 SER Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain F residue 38 ASP Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 0.0370 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 9.9990 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 6.9990 chunk 5 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 overall best weight: 1.6064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 24 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 42 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.5131 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 4440 Z= 0.173 Angle : 0.621 7.645 6012 Z= 0.338 Chirality : 0.048 0.143 630 Planarity : 0.004 0.036 774 Dihedral : 5.685 24.191 573 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.25 % Favored : 92.75 % Rotamer: Outliers : 3.05 % Allowed : 17.07 % Favored : 79.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.81 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.89 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 60 HIS 0.002 0.001 HIS D 31 PHE 0.021 0.002 PHE C 22 TYR 0.014 0.002 TYR D 63 ARG 0.006 0.000 ARG B 81 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1020 Ramachandran restraints generated. 510 Oldfield, 0 Emsley, 510 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 76 time to evaluate : 0.549 Fit side-chains REVERT: A 40 LEU cc_start: 0.9350 (OUTLIER) cc_final: 0.9091 (tt) REVERT: B 81 ARG cc_start: 0.7605 (ttm110) cc_final: 0.7333 (mtm180) REVERT: C 16 GLU cc_start: 0.7390 (mp0) cc_final: 0.6247 (tp30) REVERT: C 40 LEU cc_start: 0.9283 (OUTLIER) cc_final: 0.8970 (tt) REVERT: F 89 GLN cc_start: 0.6371 (tt0) cc_final: 0.5679 (mt0) outliers start: 15 outliers final: 12 residues processed: 82 average time/residue: 0.1370 time to fit residues: 14.8818 Evaluate side-chains 90 residues out of total 492 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 SER Chi-restraints excluded: chain A residue 38 ASP Chi-restraints excluded: chain A residue 40 LEU Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain B residue 38 ASP Chi-restraints excluded: chain B residue 49 VAL Chi-restraints excluded: chain B residue 76 ASP Chi-restraints excluded: chain C residue 40 LEU Chi-restraints excluded: chain C residue 55 SER Chi-restraints excluded: chain D residue 38 ASP Chi-restraints excluded: chain D residue 49 VAL Chi-restraints excluded: chain D residue 76 ASP Chi-restraints excluded: chain E residue 76 ASP Chi-restraints excluded: chain F residue 49 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 6.9990 chunk 15 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 7 optimal weight: 9.9990 chunk 33 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 27 optimal weight: 9.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 20.0000 chunk 32 optimal weight: 0.0970 overall best weight: 2.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 24 ASN ** 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 = 0.4404 r_free = 0.4404 target = 0.131460 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4085 r_free = 0.4085 target = 0.109238 restraints weight = 6737.217| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 3.11 r_work: 0.3946 rms_B_bonded: 3.31 restraints_weight: 0.5000 r_work (final): 0.3946 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7804 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4440 Z= 0.220 Angle : 0.640 7.589 6012 Z= 0.354 Chirality : 0.049 0.158 630 Planarity : 0.004 0.036 774 Dihedral : 5.745 26.051 573 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.22 % Favored : 90.78 % Rotamer: Outliers : 3.66 % Allowed : 16.67 % Favored : 79.67 % 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: -3.85 (0.27), residues: 510 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.92 (0.21), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP A 60 HIS 0.002 0.001 HIS D 31 PHE 0.023 0.002 PHE C 22 TYR 0.015 0.002 TYR D 63 ARG 0.006 0.000 ARG B 81 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1384.91 seconds wall clock time: 25 minutes 36.94 seconds (1536.94 seconds total)