Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 06:08:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/04_2023/8equ_28546_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/04_2023/8equ_28546.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/04_2023/8equ_28546.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/04_2023/8equ_28546.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/04_2023/8equ_28546_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8equ_28546/04_2023/8equ_28546_neut_updated.pdb" } resolution = 2.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= 0.003 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 32 5.16 5 C 3680 2.51 5 N 976 2.21 5 O 1074 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ASP 173": "OD1" <-> "OD2" Residue "B ASP 173": "OD1" <-> "OD2" Residue "C GLU 80": "OE1" <-> "OE2" Residue "F GLU 80": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5764 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1563 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "B" Number of atoms: 1563 Number of conformers: 1 Conformer: "" Number of residues, atoms: 191, 1563 Classifications: {'peptide': 191} Link IDs: {'PTRANS': 4, 'TRANS': 186} Chain breaks: 1 Chain: "C" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 506 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "D" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "E" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "F" Number of atoms: 506 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 506 Classifications: {'peptide': 80} Incomplete info: {'truncation_to_alanine': 31} Link IDs: {'PTRANS': 5, 'TRANS': 74} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 105 Unresolved non-hydrogen angles: 134 Unresolved non-hydrogen dihedrals: 88 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'TYR:plan': 1, 'GLU:plan': 5, 'ASN:plan1': 2, 'TRP:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 51 Chain: "G" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "H" Number of atoms: 395 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 395 Classifications: {'peptide': 79} Incomplete info: {'truncation_to_alanine': 79} Link IDs: {'TRANS': 78} Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 237 Unresolved non-hydrogen dihedrals: 79 Planarities with less than four sites: {'UNK:plan-1': 79} Unresolved non-hydrogen planarities: 79 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'PEE': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 28 Unresolved non-hydrogen angles: 28 Unresolved non-hydrogen dihedrals: 28 Time building chain proxies: 3.77, per 1000 atoms: 0.65 Number of scatterers: 5764 At special positions: 0 Unit cell: (90.308, 93.684, 89.464, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 32 16.00 P 2 15.00 O 1074 8.00 N 976 7.00 C 3680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 4 " - pdb=" SG CYS C 79 " distance=2.03 Simple disulfide: pdb=" SG CYS C 7 " - pdb=" SG CYS C 73 " distance=2.03 Simple disulfide: pdb=" SG CYS C 35 " - pdb=" SG CYS C 47 " distance=2.03 Simple disulfide: pdb=" SG CYS F 4 " - pdb=" SG CYS F 79 " distance=2.03 Simple disulfide: pdb=" SG CYS F 7 " - pdb=" SG CYS F 73 " distance=2.03 Simple disulfide: pdb=" SG CYS F 35 " - pdb=" SG CYS F 47 " 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: 2.51 Conformation dependent library (CDL) restraints added in 783.5 milliseconds 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1668 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 2 sheets defined 105.9% alpha, 15.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'A' and resid 43 through 62 removed outlier: 3.754A pdb=" N LYS A 61 " --> pdb=" O SER A 58 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 98 Processing helix chain 'A' and resid 106 through 133 Processing helix chain 'A' and resid 136 through 140 Processing helix chain 'B' and resid 43 through 62 removed outlier: 3.755A pdb=" N LYS B 61 " --> pdb=" O SER B 58 " (cutoff:3.500A) Processing helix chain 'B' and resid 68 through 98 Processing helix chain 'B' and resid 106 through 133 Processing helix chain 'B' and resid 136 through 140 Processing helix chain 'C' and resid 2 through 18 removed outlier: 3.502A pdb=" N ILE C 6 " --> pdb=" O LEU C 2 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 36 removed outlier: 3.528A pdb=" N CYS C 35 " --> pdb=" O LEU C 31 " (cutoff:3.500A) Processing helix chain 'C' and resid 43 through 66 removed outlier: 4.298A pdb=" N ASP C 52 " --> pdb=" O LYS C 48 " (cutoff:3.500A) Proline residue: C 56 - end of helix Processing helix chain 'C' and resid 69 through 76 removed outlier: 3.561A pdb=" N LEU C 76 " --> pdb=" O VAL C 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 18 Processing helix chain 'D' and resid 21 through 37 removed outlier: 3.731A pdb=" N UNK D 37 " --> pdb=" O UNK D 33 " (cutoff:3.500A) Processing helix chain 'D' and resid 41 through 75 removed outlier: 4.055A pdb=" N UNK D 46 " --> pdb=" O UNK D 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK D 56 " --> pdb=" O UNK D 52 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N UNK D 57 " --> pdb=" O UNK D 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK D 68 " --> pdb=" O UNK D 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N UNK D 69 " --> pdb=" O UNK D 65 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N UNK D 70 " --> pdb=" O UNK D 66 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N UNK D 71 " --> pdb=" O UNK D 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 2 through 18 Processing helix chain 'E' and resid 21 through 37 removed outlier: 3.732A pdb=" N UNK E 37 " --> pdb=" O UNK E 33 " (cutoff:3.500A) Processing helix chain 'E' and resid 41 through 75 removed outlier: 4.055A pdb=" N UNK E 46 " --> pdb=" O UNK E 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK E 56 " --> pdb=" O UNK E 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK E 57 " --> pdb=" O UNK E 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N UNK E 68 " --> pdb=" O UNK E 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N UNK E 69 " --> pdb=" O UNK E 65 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N UNK E 70 " --> pdb=" O UNK E 66 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N UNK E 71 " --> pdb=" O UNK E 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 2 through 18 removed outlier: 3.501A pdb=" N ILE F 6 " --> pdb=" O LEU F 2 " (cutoff:3.500A) Processing helix chain 'F' and resid 21 through 36 removed outlier: 3.529A pdb=" N CYS F 35 " --> pdb=" O LEU F 31 " (cutoff:3.500A) Processing helix chain 'F' and resid 43 through 66 removed outlier: 4.298A pdb=" N ASP F 52 " --> pdb=" O LYS F 48 " (cutoff:3.500A) Proline residue: F 56 - end of helix Processing helix chain 'F' and resid 69 through 76 removed outlier: 3.560A pdb=" N LEU F 76 " --> pdb=" O VAL F 72 " (cutoff:3.500A) Processing helix chain 'G' and resid 2 through 18 Processing helix chain 'G' and resid 21 through 37 removed outlier: 3.732A pdb=" N UNK G 37 " --> pdb=" O UNK G 33 " (cutoff:3.500A) Processing helix chain 'G' and resid 41 through 75 removed outlier: 4.055A pdb=" N UNK G 46 " --> pdb=" O UNK G 42 " (cutoff:3.500A) removed outlier: 3.983A pdb=" N UNK G 56 " --> pdb=" O UNK G 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK G 57 " --> pdb=" O UNK G 53 " (cutoff:3.500A) removed outlier: 3.841A pdb=" N UNK G 68 " --> pdb=" O UNK G 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N UNK G 69 " --> pdb=" O UNK G 65 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N UNK G 70 " --> pdb=" O UNK G 66 " (cutoff:3.500A) removed outlier: 6.997A pdb=" N UNK G 71 " --> pdb=" O UNK G 67 " (cutoff:3.500A) Processing helix chain 'H' and resid 2 through 18 Processing helix chain 'H' and resid 21 through 37 removed outlier: 3.732A pdb=" N UNK H 37 " --> pdb=" O UNK H 33 " (cutoff:3.500A) Processing helix chain 'H' and resid 41 through 75 removed outlier: 4.055A pdb=" N UNK H 46 " --> pdb=" O UNK H 42 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N UNK H 56 " --> pdb=" O UNK H 52 " (cutoff:3.500A) removed outlier: 4.325A pdb=" N UNK H 57 " --> pdb=" O UNK H 53 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N UNK H 68 " --> pdb=" O UNK H 64 " (cutoff:3.500A) removed outlier: 4.387A pdb=" N UNK H 69 " --> pdb=" O UNK H 65 " (cutoff:3.500A) removed outlier: 6.520A pdb=" N UNK H 70 " --> pdb=" O UNK H 66 " (cutoff:3.500A) removed outlier: 6.998A pdb=" N UNK H 71 " --> pdb=" O UNK H 67 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 155 through 160 removed outlier: 6.193A pdb=" N HIS A 150 " --> pdb=" O CYS A 200 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N CYS A 200 " --> pdb=" O HIS A 150 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE A 232 " --> pdb=" O TYR A 215 " (cutoff:3.500A) removed outlier: 4.488A pdb=" N THR A 217 " --> pdb=" O PHE A 230 " (cutoff:3.500A) removed outlier: 6.487A pdb=" N PHE A 230 " --> pdb=" O THR A 217 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 155 through 160 removed outlier: 6.194A pdb=" N HIS B 150 " --> pdb=" O CYS B 200 " (cutoff:3.500A) removed outlier: 8.447A pdb=" N CYS B 200 " --> pdb=" O HIS B 150 " (cutoff:3.500A) removed outlier: 6.909A pdb=" N ILE B 232 " --> pdb=" O TYR B 215 " (cutoff:3.500A) removed outlier: 4.489A pdb=" N THR B 217 " --> pdb=" O PHE B 230 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N PHE B 230 " --> pdb=" O THR B 217 " (cutoff:3.500A) 480 hydrogen bonds defined for protein. 1314 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: 1.71 Time building geometry restraints manager: 2.58 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 966 1.32 - 1.44: 1530 1.44 - 1.57: 3320 1.57 - 1.70: 4 1.70 - 1.82: 38 Bond restraints: 5858 Sorted by residual: bond pdb=" C10 PEE B 401 " pdb=" O2 PEE B 401 " ideal model delta sigma weight residual 1.332 1.429 -0.097 2.00e-02 2.50e+03 2.34e+01 bond pdb=" C10 PEE A 401 " pdb=" O2 PEE A 401 " ideal model delta sigma weight residual 1.332 1.428 -0.096 2.00e-02 2.50e+03 2.29e+01 bond pdb=" C30 PEE A 401 " pdb=" O3 PEE A 401 " ideal model delta sigma weight residual 1.327 1.411 -0.084 2.00e-02 2.50e+03 1.77e+01 bond pdb=" C30 PEE B 401 " pdb=" O3 PEE B 401 " ideal model delta sigma weight residual 1.327 1.411 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C LEU A 41 " pdb=" N PRO A 42 " ideal model delta sigma weight residual 1.333 1.358 -0.025 1.01e-02 9.80e+03 5.99e+00 ... (remaining 5853 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.94: 66 105.94 - 112.95: 3274 112.95 - 119.97: 1870 119.97 - 126.99: 2773 126.99 - 134.00: 57 Bond angle restraints: 8040 Sorted by residual: angle pdb=" O3P PEE B 401 " pdb=" P PEE B 401 " pdb=" O4P PEE B 401 " ideal model delta sigma weight residual 92.91 109.35 -16.44 3.00e+00 1.11e-01 3.00e+01 angle pdb=" O3P PEE A 401 " pdb=" P PEE A 401 " pdb=" O4P PEE A 401 " ideal model delta sigma weight residual 92.91 109.31 -16.40 3.00e+00 1.11e-01 2.99e+01 angle pdb=" CB MET A 125 " pdb=" CG MET A 125 " pdb=" SD MET A 125 " ideal model delta sigma weight residual 112.70 122.43 -9.73 3.00e+00 1.11e-01 1.05e+01 angle pdb=" CB MET B 125 " pdb=" CG MET B 125 " pdb=" SD MET B 125 " ideal model delta sigma weight residual 112.70 122.40 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" O1P PEE A 401 " pdb=" P PEE A 401 " pdb=" O2P PEE A 401 " ideal model delta sigma weight residual 119.43 109.80 9.63 3.00e+00 1.11e-01 1.03e+01 ... (remaining 8035 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.03: 3216 17.03 - 34.07: 170 34.07 - 51.10: 20 51.10 - 68.13: 14 68.13 - 85.16: 10 Dihedral angle restraints: 3430 sinusoidal: 880 harmonic: 2550 Sorted by residual: dihedral pdb=" CB CYS F 4 " pdb=" SG CYS F 4 " pdb=" SG CYS F 79 " pdb=" CB CYS F 79 " ideal model delta sinusoidal sigma weight residual -86.00 -171.16 85.16 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CB CYS C 4 " pdb=" SG CYS C 4 " pdb=" SG CYS C 79 " pdb=" CB CYS C 79 " ideal model delta sinusoidal sigma weight residual -86.00 -171.14 85.14 1 1.00e+01 1.00e-02 8.79e+01 dihedral pdb=" CB CYS C 35 " pdb=" SG CYS C 35 " pdb=" SG CYS C 47 " pdb=" CB CYS C 47 " ideal model delta sinusoidal sigma weight residual -86.00 -145.66 59.66 1 1.00e+01 1.00e-02 4.75e+01 ... (remaining 3427 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 821 0.048 - 0.096: 159 0.096 - 0.144: 20 0.144 - 0.193: 0 0.193 - 0.241: 2 Chirality restraints: 1002 Sorted by residual: chirality pdb=" C2 PEE A 401 " pdb=" C1 PEE A 401 " pdb=" C3 PEE A 401 " pdb=" O2 PEE A 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.57 0.24 2.00e-01 2.50e+01 1.45e+00 chirality pdb=" C2 PEE B 401 " pdb=" C1 PEE B 401 " pdb=" C3 PEE B 401 " pdb=" O2 PEE B 401 " both_signs ideal model delta sigma weight residual False -2.33 -2.57 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA ILE A 169 " pdb=" N ILE A 169 " pdb=" C ILE A 169 " pdb=" CB ILE A 169 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.70e-01 ... (remaining 999 not shown) Planarity restraints: 1022 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 41 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.54e+00 pdb=" C LEU B 41 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU B 41 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO B 42 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 41 " -0.011 2.00e-02 2.50e+03 2.13e-02 4.53e+00 pdb=" C LEU A 41 " 0.037 2.00e-02 2.50e+03 pdb=" O LEU A 41 " -0.013 2.00e-02 2.50e+03 pdb=" N PRO A 42 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 206 " 0.011 2.00e-02 2.50e+03 1.13e-02 2.55e+00 pdb=" CG TYR B 206 " -0.028 2.00e-02 2.50e+03 pdb=" CD1 TYR B 206 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR B 206 " 0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR B 206 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 206 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 206 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 206 " -0.001 2.00e-02 2.50e+03 ... (remaining 1019 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 1960 2.83 - 3.35: 5929 3.35 - 3.87: 9621 3.87 - 4.38: 9986 4.38 - 4.90: 17462 Nonbonded interactions: 44958 Sorted by model distance: nonbonded pdb=" O LYS A 198 " pdb=" OH TYR A 233 " model vdw 2.317 2.440 nonbonded pdb=" O LYS B 198 " pdb=" OH TYR B 233 " model vdw 2.317 2.440 nonbonded pdb=" OH TYR B 154 " pdb=" OE2 GLU B 191 " model vdw 2.344 2.440 nonbonded pdb=" OH TYR A 154 " pdb=" OE2 GLU A 191 " model vdw 2.344 2.440 nonbonded pdb=" OG1 THR A 164 " pdb=" O SER A 166 " model vdw 2.344 2.440 ... (remaining 44953 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' } ncs_group { reference = chain 'C' selection = chain 'F' } ncs_group { reference = chain 'D' selection = chain 'E' selection = chain 'G' selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.700 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: 3.840 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.220 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.040 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:11.470 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.770 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 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 : 0.004 0.097 5858 Z= 0.261 Angle : 0.790 16.435 8040 Z= 0.382 Chirality : 0.040 0.241 1002 Planarity : 0.004 0.032 1022 Dihedral : 12.393 83.216 1744 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 0.00 % 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: -0.12 (0.36), residues: 530 helix: 0.76 (0.30), residues: 308 sheet: -0.26 (0.51), residues: 92 loop : -1.82 (0.49), residues: 130 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 99 time to evaluate : 0.538 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 0.8878 time to fit residues: 93.0611 Evaluate side-chains 71 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 71 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6885 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 69 optimal weight: 20.0000 chunk 62 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 64 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 93 HIS B 82 ASN B 93 HIS F 77 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7399 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.047 5858 Z= 0.429 Angle : 0.588 7.497 8040 Z= 0.303 Chirality : 0.039 0.137 1002 Planarity : 0.005 0.035 1022 Dihedral : 6.982 80.878 908 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 1.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.40 (0.36), residues: 530 helix: 1.30 (0.29), residues: 310 sheet: -0.61 (0.51), residues: 94 loop : -1.52 (0.51), residues: 126 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 74 time to evaluate : 0.558 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 80 average time/residue: 1.0105 time to fit residues: 85.2149 Evaluate side-chains 71 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 67 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 2 residues processed: 2 average time/residue: 0.1945 time to fit residues: 1.1679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 41 optimal weight: 0.8980 chunk 23 optimal weight: 0.5980 chunk 61 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 20 optimal weight: 0.6980 chunk 74 optimal weight: 20.0000 chunk 80 optimal weight: 20.0000 chunk 66 optimal weight: 6.9990 chunk 73 optimal weight: 10.0000 chunk 25 optimal weight: 0.1980 chunk 59 optimal weight: 30.0000 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN B 82 ASN F 77 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5858 Z= 0.184 Angle : 0.481 6.569 8040 Z= 0.247 Chirality : 0.034 0.122 1002 Planarity : 0.004 0.032 1022 Dihedral : 6.069 79.219 908 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer Outliers : 0.93 % 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: 0.62 (0.37), residues: 530 helix: 1.54 (0.30), residues: 308 sheet: -0.67 (0.52), residues: 94 loop : -1.42 (0.51), residues: 128 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.573 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 0.9079 time to fit residues: 70.4137 Evaluate side-chains 67 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 65 time to evaluate : 0.554 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1881 time to fit residues: 1.1615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 73 optimal weight: 20.0000 chunk 56 optimal weight: 20.0000 chunk 38 optimal weight: 0.0870 chunk 8 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 50 optimal weight: 20.0000 chunk 74 optimal weight: 20.0000 chunk 79 optimal weight: 30.0000 chunk 39 optimal weight: 5.9990 chunk 70 optimal weight: 20.0000 chunk 21 optimal weight: 3.9990 overall best weight: 2.7364 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 116 GLN B 119 ASN F 77 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.3510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.061 5858 Z= 0.571 Angle : 0.626 8.395 8040 Z= 0.317 Chirality : 0.040 0.149 1002 Planarity : 0.004 0.036 1022 Dihedral : 5.643 68.270 908 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 2.10 % 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: 0.19 (0.36), residues: 530 helix: 1.10 (0.29), residues: 310 sheet: -0.66 (0.51), residues: 94 loop : -1.53 (0.50), residues: 126 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 76 time to evaluate : 0.575 Fit side-chains outliers start: 9 outliers final: 3 residues processed: 83 average time/residue: 0.9821 time to fit residues: 86.1856 Evaluate side-chains 75 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 72 time to evaluate : 0.665 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.2053 time to fit residues: 1.2488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 66 optimal weight: 7.9990 chunk 44 optimal weight: 0.5980 chunk 1 optimal weight: 0.7980 chunk 59 optimal weight: 30.0000 chunk 32 optimal weight: 0.6980 chunk 67 optimal weight: 0.7980 chunk 54 optimal weight: 20.0000 chunk 0 optimal weight: 1.9990 chunk 40 optimal weight: 8.9990 chunk 71 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.3437 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5858 Z= 0.204 Angle : 0.502 8.191 8040 Z= 0.254 Chirality : 0.034 0.120 1002 Planarity : 0.004 0.033 1022 Dihedral : 5.542 71.740 908 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 7.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 1.64 % 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 (0.37), residues: 530 helix: 1.49 (0.30), residues: 306 sheet: -0.80 (0.51), residues: 94 loop : -1.22 (0.52), residues: 130 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.511 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 78 average time/residue: 0.8458 time to fit residues: 70.2384 Evaluate side-chains 74 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 69 time to evaluate : 0.570 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.1894 time to fit residues: 1.1911 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 26 optimal weight: 0.8980 chunk 71 optimal weight: 10.0000 chunk 15 optimal weight: 0.2980 chunk 46 optimal weight: 30.0000 chunk 19 optimal weight: 0.9980 chunk 79 optimal weight: 30.0000 chunk 65 optimal weight: 8.9990 chunk 36 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 41 optimal weight: 30.0000 chunk 76 optimal weight: 20.0000 overall best weight: 1.4382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 119 ASN B 82 ASN B 116 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7427 moved from start: 0.3853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.036 5858 Z= 0.338 Angle : 0.548 8.249 8040 Z= 0.275 Chirality : 0.036 0.133 1002 Planarity : 0.004 0.033 1022 Dihedral : 5.574 71.828 908 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 2.80 % 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: 0.58 (0.37), residues: 530 helix: 1.48 (0.30), residues: 306 sheet: -0.91 (0.52), residues: 90 loop : -1.14 (0.52), residues: 134 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 69 time to evaluate : 0.593 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 79 average time/residue: 0.7704 time to fit residues: 65.3198 Evaluate side-chains 75 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 69 time to evaluate : 0.557 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.1973 time to fit residues: 1.1826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 8 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 57 optimal weight: 30.0000 chunk 44 optimal weight: 6.9990 chunk 66 optimal weight: 4.9990 chunk 79 optimal weight: 30.0000 chunk 49 optimal weight: 10.0000 chunk 48 optimal weight: 10.0000 chunk 36 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 20.0000 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 116 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.4564 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.010 0.070 5858 Z= 0.648 Angle : 0.681 9.023 8040 Z= 0.341 Chirality : 0.041 0.158 1002 Planarity : 0.004 0.035 1022 Dihedral : 5.753 68.313 908 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer Outliers : 4.21 % 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: 0.28 (0.36), residues: 530 helix: 1.14 (0.30), residues: 306 sheet: -0.80 (0.54), residues: 90 loop : -1.15 (0.51), residues: 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.573 Fit side-chains outliers start: 18 outliers final: 10 residues processed: 91 average time/residue: 0.9018 time to fit residues: 86.9180 Evaluate side-chains 79 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 69 time to evaluate : 0.559 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 6 residues processed: 4 average time/residue: 0.1221 time to fit residues: 1.3599 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 23 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 30.0000 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 71 optimal weight: 10.0000 chunk 75 optimal weight: 30.0000 chunk 69 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 overall best weight: 2.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.4703 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.058 5858 Z= 0.520 Angle : 0.636 9.659 8040 Z= 0.318 Chirality : 0.038 0.143 1002 Planarity : 0.004 0.036 1022 Dihedral : 5.809 68.870 908 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 8.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 3.04 % 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: 0.27 (0.36), residues: 530 helix: 1.17 (0.29), residues: 306 sheet: -0.85 (0.52), residues: 94 loop : -1.23 (0.51), residues: 130 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.571 Fit side-chains outliers start: 13 outliers final: 7 residues processed: 81 average time/residue: 0.8899 time to fit residues: 76.5311 Evaluate side-chains 76 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 69 time to evaluate : 0.566 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1862 time to fit residues: 1.1117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 75 optimal weight: 30.0000 chunk 44 optimal weight: 0.4980 chunk 32 optimal weight: 0.8980 chunk 57 optimal weight: 30.0000 chunk 22 optimal weight: 0.8980 chunk 66 optimal weight: 8.9990 chunk 69 optimal weight: 20.0000 chunk 73 optimal weight: 20.0000 chunk 48 optimal weight: 20.0000 chunk 77 optimal weight: 30.0000 chunk 47 optimal weight: 20.0000 overall best weight: 6.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 82 ASN B 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7528 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.019 0.137 5858 Z= 1.221 Angle : 0.962 11.051 8040 Z= 0.477 Chirality : 0.055 0.237 1002 Planarity : 0.006 0.040 1022 Dihedral : 6.215 65.853 908 Min Nonbonded Distance : 2.028 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer Outliers : 2.80 % 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: -0.09 (0.36), residues: 530 helix: 0.63 (0.29), residues: 302 sheet: -0.72 (0.52), residues: 102 loop : -0.82 (0.53), residues: 126 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.563 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 80 average time/residue: 1.0824 time to fit residues: 91.2873 Evaluate side-chains 75 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 67 time to evaluate : 0.580 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.7218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 36 optimal weight: 0.9990 chunk 54 optimal weight: 20.0000 chunk 81 optimal weight: 20.0000 chunk 75 optimal weight: 20.0000 chunk 65 optimal weight: 8.9990 chunk 6 optimal weight: 1.9990 chunk 50 optimal weight: 20.0000 chunk 39 optimal weight: 0.8980 chunk 51 optimal weight: 10.0000 chunk 69 optimal weight: 20.0000 chunk 19 optimal weight: 0.7980 overall best weight: 2.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 GLN B 116 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.5462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.063 5858 Z= 0.580 Angle : 0.697 10.500 8040 Z= 0.347 Chirality : 0.040 0.162 1002 Planarity : 0.005 0.038 1022 Dihedral : 5.907 66.298 908 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer Outliers : 2.10 % 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: 0.02 (0.36), residues: 530 helix: 0.80 (0.29), residues: 308 sheet: -0.79 (0.52), residues: 102 loop : -1.01 (0.53), residues: 120 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1060 Ramachandran restraints generated. 530 Oldfield, 0 Emsley, 530 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.596 Fit side-chains outliers start: 9 outliers final: 10 residues processed: 75 average time/residue: 0.9225 time to fit residues: 73.2949 Evaluate side-chains 76 residues out of total 490 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.551 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 2 average time/residue: 0.1720 time to fit residues: 1.0948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 82 random chunks: chunk 59 optimal weight: 20.0000 chunk 9 optimal weight: 0.0870 chunk 18 optimal weight: 0.6980 chunk 65 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.7980 chunk 57 optimal weight: 30.0000 chunk 3 optimal weight: 0.9990 chunk 47 optimal weight: 20.0000 overall best weight: 0.6158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 82 ASN A 116 GLN B 82 ASN B 116 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4256 r_free = 0.4256 target = 0.188422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.111833 restraints weight = 6927.973| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.40 r_work: 0.3028 rms_B_bonded: 3.24 restraints_weight: 0.5000 r_work: 0.2863 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.2863 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 5858 Z= 0.199 Angle : 0.572 9.688 8040 Z= 0.284 Chirality : 0.034 0.119 1002 Planarity : 0.004 0.037 1022 Dihedral : 5.598 63.093 908 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.70 % Favored : 98.30 % Rotamer Outliers : 3.04 % 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: 0.23 (0.36), residues: 530 helix: 1.23 (0.29), residues: 308 sheet: -0.98 (0.52), residues: 94 loop : -1.47 (0.49), residues: 128 =============================================================================== Job complete usr+sys time: 1990.61 seconds wall clock time: 36 minutes 13.52 seconds (2173.52 seconds total)