Starting phenix.real_space_refine on Fri Mar 15 16:28:20 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t93_10408/03_2024/6t93_10408.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t93_10408/03_2024/6t93_10408.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.49 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t93_10408/03_2024/6t93_10408.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t93_10408/03_2024/6t93_10408.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t93_10408/03_2024/6t93_10408.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6t93_10408/03_2024/6t93_10408.pdb" } resolution = 3.49 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= 0.003 sd= 0.051 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 300 5.49 5 S 14 5.16 5 C 6730 2.51 5 N 2287 2.21 5 O 2868 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 55": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 73": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 89": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ASP 91": "OD1" <-> "OD2" Residue "H TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12199 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 790 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 790 Classifications: {'peptide': 96} Link IDs: {'PTRANS': 3, 'TRANS': 92} Chain: "F" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 835 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3072 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3072 Classifications: {'DNA': 151} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 150} Chain: "J" Number of atoms: 3113 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 3113 Classifications: {'DNA': 151} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 150} Time building chain proxies: 6.48, per 1000 atoms: 0.53 Number of scatterers: 12199 At special positions: 0 Unit cell: (73.96, 121.26, 117.82, 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 14 16.00 P 300 15.00 O 2868 8.00 N 2287 7.00 C 6730 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.51 Conformation dependent library (CDL) restraints added in 1.2 seconds 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1412 Finding SS restraints... Secondary structure from input PDB file: 35 helices and 10 sheets defined 70.7% alpha, 2.9% beta 151 base pairs and 279 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 45 through 58 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 115 Processing helix chain 'A' and resid 121 through 132 removed outlier: 3.502A pdb=" N ILE A 125 " --> pdb=" O MET A 121 " (cutoff:3.500A) Processing helix chain 'B' and resid 26 through 30 Processing helix chain 'B' and resid 31 through 42 Processing helix chain 'B' and resid 50 through 77 Processing helix chain 'B' and resid 83 through 93 Processing helix chain 'C' and resid 17 through 23 removed outlier: 3.717A pdb=" N ARG C 21 " --> pdb=" O THR C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 37 Processing helix chain 'C' and resid 47 through 74 Processing helix chain 'C' and resid 80 through 90 Processing helix chain 'C' and resid 91 through 98 Processing helix chain 'C' and resid 113 through 117 Processing helix chain 'D' and resid 38 through 50 Processing helix chain 'D' and resid 56 through 85 Processing helix chain 'D' and resid 91 through 103 Processing helix chain 'D' and resid 104 through 125 Processing helix chain 'E' and resid 45 through 58 removed outlier: 3.530A pdb=" N ARG E 50 " --> pdb=" O THR E 46 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 77 removed outlier: 3.699A pdb=" N PHE E 68 " --> pdb=" O ARG E 64 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 115 Processing helix chain 'E' and resid 121 through 132 Processing helix chain 'F' and resid 31 through 42 Processing helix chain 'F' and resid 50 through 77 removed outlier: 3.598A pdb=" N GLU F 54 " --> pdb=" O LEU F 50 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 93 removed outlier: 3.519A pdb=" N ARG F 93 " --> pdb=" O TYR F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 22 removed outlier: 3.571A pdb=" N ARG G 21 " --> pdb=" O THR G 17 " (cutoff:3.500A) Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 47 through 73 Processing helix chain 'G' and resid 80 through 91 Processing helix chain 'G' and resid 93 through 98 Processing helix chain 'G' and resid 113 through 117 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 104 through 125 removed outlier: 3.535A pdb=" N HIS H 110 " --> pdb=" O GLU H 106 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 84 through 85 removed outlier: 7.007A pdb=" N ARG A 84 " --> pdb=" O VAL B 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 119 through 120 Processing sheet with id=AA3, first strand: chain 'B' and resid 98 through 99 Processing sheet with id=AA4, first strand: chain 'C' and resid 43 through 44 removed outlier: 7.190A pdb=" N ARG C 43 " --> pdb=" O ILE D 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 78 through 79 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 103 Processing sheet with id=AA7, first strand: chain 'E' and resid 84 through 85 removed outlier: 6.887A pdb=" N ARG E 84 " --> pdb=" O VAL F 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 119 through 120 Processing sheet with id=AA9, first strand: chain 'G' and resid 43 through 44 removed outlier: 7.000A pdb=" N ARG G 43 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 78 through 79 398 hydrogen bonds defined for protein. 1176 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 380 hydrogen bonds 760 hydrogen bond angles 0 basepair planarities 151 basepair parallelities 279 stacking parallelities Total time for adding SS restraints: 4.37 Time building geometry restraints manager: 6.83 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1888 1.32 - 1.44: 4716 1.44 - 1.57: 5804 1.57 - 1.69: 600 1.69 - 1.81: 24 Bond restraints: 13032 Sorted by residual: bond pdb=" CD ARG E 129 " pdb=" NE ARG E 129 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.05e+01 bond pdb=" CD ARG D 100 " pdb=" NE ARG D 100 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.03e+01 bond pdb=" CD ARG B 93 " pdb=" NE ARG B 93 " ideal model delta sigma weight residual 1.458 1.395 0.063 1.40e-02 5.10e+03 2.00e+01 bond pdb=" CD ARG A 129 " pdb=" NE ARG A 129 " ideal model delta sigma weight residual 1.458 1.396 0.062 1.40e-02 5.10e+03 1.96e+01 bond pdb=" CD ARG F 93 " pdb=" NE ARG F 93 " ideal model delta sigma weight residual 1.458 1.398 0.060 1.40e-02 5.10e+03 1.86e+01 ... (remaining 13027 not shown) Histogram of bond angle deviations from ideal: 97.93 - 105.01: 1299 105.01 - 112.08: 7139 112.08 - 119.16: 3720 119.16 - 126.24: 5913 126.24 - 133.31: 822 Bond angle restraints: 18893 Sorted by residual: angle pdb=" C HIS D 50 " pdb=" N PRO D 51 " pdb=" CA PRO D 51 " ideal model delta sigma weight residual 119.56 127.54 -7.98 1.02e+00 9.61e-01 6.12e+01 angle pdb=" C HIS H 50 " pdb=" N PRO H 51 " pdb=" CA PRO H 51 " ideal model delta sigma weight residual 119.56 127.23 -7.67 1.02e+00 9.61e-01 5.66e+01 angle pdb=" C LEU D 103 " pdb=" N PRO D 104 " pdb=" CA PRO D 104 " ideal model delta sigma weight residual 119.78 126.98 -7.20 1.03e+00 9.43e-01 4.88e+01 angle pdb=" C PHE C 26 " pdb=" N PRO C 27 " pdb=" CA PRO C 27 " ideal model delta sigma weight residual 119.76 126.26 -6.50 1.00e+00 1.00e+00 4.22e+01 angle pdb=" C ILE G 80 " pdb=" N PRO G 81 " pdb=" CA PRO G 81 " ideal model delta sigma weight residual 119.32 126.49 -7.17 1.14e+00 7.69e-01 3.95e+01 ... (remaining 18888 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.25: 5714 34.25 - 68.50: 1356 68.50 - 102.75: 12 102.75 - 137.00: 0 137.00 - 171.25: 4 Dihedral angle restraints: 7086 sinusoidal: 4894 harmonic: 2192 Sorted by residual: dihedral pdb=" C4' DT J 89 " pdb=" C3' DT J 89 " pdb=" O3' DT J 89 " pdb=" P DA J 90 " ideal model delta sinusoidal sigma weight residual 220.00 48.75 171.25 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual 220.00 56.09 163.91 1 3.50e+01 8.16e-04 1.54e+01 dihedral pdb=" C4' DG I 3 " pdb=" C3' DG I 3 " pdb=" O3' DG I 3 " pdb=" P DG I 4 " ideal model delta sinusoidal sigma weight residual 220.00 63.58 156.42 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7083 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.063: 1519 0.063 - 0.127: 549 0.127 - 0.190: 70 0.190 - 0.253: 6 0.253 - 0.317: 2 Chirality restraints: 2146 Sorted by residual: chirality pdb=" CA LYS F 32 " pdb=" N LYS F 32 " pdb=" C LYS F 32 " pdb=" CB LYS F 32 " both_signs ideal model delta sigma weight residual False 2.51 2.19 0.32 2.00e-01 2.50e+01 2.50e+00 chirality pdb=" CA LEU A 66 " pdb=" N LEU A 66 " pdb=" C LEU A 66 " pdb=" CB LEU A 66 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.89e+00 chirality pdb=" CA LYS B 32 " pdb=" N LYS B 32 " pdb=" C LYS B 32 " pdb=" CB LYS B 32 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.60e+00 ... (remaining 2143 not shown) Planarity restraints: 1346 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS G 37 " -0.020 2.00e-02 2.50e+03 3.98e-02 1.59e+01 pdb=" C LYS G 37 " 0.069 2.00e-02 2.50e+03 pdb=" O LYS G 37 " -0.026 2.00e-02 2.50e+03 pdb=" N GLY G 38 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR F 52 " 0.055 2.00e-02 2.50e+03 2.79e-02 1.55e+01 pdb=" CG TYR F 52 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 TYR F 52 " -0.026 2.00e-02 2.50e+03 pdb=" CD2 TYR F 52 " -0.017 2.00e-02 2.50e+03 pdb=" CE1 TYR F 52 " 0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR F 52 " -0.007 2.00e-02 2.50e+03 pdb=" CZ TYR F 52 " 0.009 2.00e-02 2.50e+03 pdb=" OH TYR F 52 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLY B 103 " -0.019 2.00e-02 2.50e+03 3.90e-02 1.52e+01 pdb=" C GLY B 103 " 0.067 2.00e-02 2.50e+03 pdb=" O GLY B 103 " -0.024 2.00e-02 2.50e+03 pdb=" OXT GLY B 103 " -0.024 2.00e-02 2.50e+03 ... (remaining 1343 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 4776 2.93 - 3.42: 10638 3.42 - 3.91: 24618 3.91 - 4.41: 29004 4.41 - 4.90: 36678 Nonbonded interactions: 105714 Sorted by model distance: nonbonded pdb=" NZ LYS F 60 " pdb=" OE2 GLU F 64 " model vdw 2.435 2.520 nonbonded pdb=" O ARG A 43 " pdb=" OG1 THR A 46 " model vdw 2.481 2.440 nonbonded pdb=" N GLY C 38 " pdb=" N ASN C 39 " model vdw 2.491 2.560 nonbonded pdb=" N GLY G 38 " pdb=" N ASN G 39 " model vdw 2.493 2.560 nonbonded pdb=" N ASP D 52 " pdb=" OD1 ASP D 52 " model vdw 2.497 2.520 ... (remaining 105709 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 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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=0.00 max=1.00 mean=0.99 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: 1.650 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: 4.200 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 39.680 Find NCS groups from input model: 0.440 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: 0.010 Load rotamer database and sin/cos tables:2.300 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 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 : 0.014 0.118 13032 Z= 0.908 Angle : 1.153 9.394 18893 Z= 0.772 Chirality : 0.062 0.317 2146 Planarity : 0.010 0.069 1346 Dihedral : 27.104 171.253 5674 Min Nonbonded Distance : 2.435 Molprobity Statistics. All-atom Clashscore : 0.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.27 % Favored : 99.73 % Rotamer: Outliers : 0.00 % Allowed : 0.16 % Favored : 99.84 % 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: 0.78 (0.26), residues: 742 helix: 0.67 (0.19), residues: 528 sheet: None (None), residues: 0 loop : 0.50 (0.36), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.013 0.003 HIS H 50 PHE 0.032 0.007 PHE D 71 TYR 0.055 0.011 TYR F 52 ARG 0.016 0.002 ARG B 37 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 308 time to evaluate : 0.951 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 75 ILE cc_start: 0.9462 (mt) cc_final: 0.9125 (mm) REVERT: A 77 GLN cc_start: 0.8200 (pt0) cc_final: 0.7993 (pp30) REVERT: A 82 ASP cc_start: 0.8647 (m-30) cc_final: 0.8388 (m-30) REVERT: A 114 HIS cc_start: 0.8772 (t70) cc_final: 0.8462 (t-90) REVERT: B 24 ARG cc_start: 0.8295 (mtm110) cc_final: 0.8031 (ppt170) REVERT: B 97 THR cc_start: 0.8583 (m) cc_final: 0.8379 (p) REVERT: C 74 ASN cc_start: 0.8984 (m-40) cc_final: 0.8406 (t0) REVERT: C 102 THR cc_start: 0.8968 (m) cc_final: 0.8690 (p) REVERT: D 35 LYS cc_start: 0.8194 (mmtt) cc_final: 0.7583 (mmtm) REVERT: D 52 ASP cc_start: 0.8489 (p0) cc_final: 0.8131 (p0) REVERT: D 60 MET cc_start: 0.9081 (tpp) cc_final: 0.8869 (tpp) REVERT: D 72 GLU cc_start: 0.8212 (mm-30) cc_final: 0.7934 (tp30) REVERT: D 80 ARG cc_start: 0.8635 (mtm-85) cc_final: 0.8274 (mtm-85) REVERT: E 104 LEU cc_start: 0.9483 (tp) cc_final: 0.9220 (tp) REVERT: E 121 MET cc_start: 0.8348 (mmm) cc_final: 0.8148 (mmm) REVERT: G 37 LYS cc_start: 0.7759 (mttm) cc_final: 0.7536 (mttp) REVERT: G 105 GLN cc_start: 0.8637 (mp10) cc_final: 0.8409 (mp10) REVERT: G 119 LYS cc_start: 0.8693 (pttt) cc_final: 0.8380 (tppt) REVERT: H 80 ARG cc_start: 0.8980 (mtm-85) cc_final: 0.8187 (mtm-85) outliers start: 0 outliers final: 0 residues processed: 308 average time/residue: 0.2593 time to fit residues: 108.9941 Evaluate side-chains 227 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 227 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 2.9990 chunk 42 optimal weight: 0.9980 chunk 26 optimal weight: 7.9990 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 3.9990 chunk 59 optimal weight: 0.0570 chunk 92 optimal weight: 5.9990 overall best weight: 1.2104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 40 HIS ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 85 GLN D 110 HIS E 40 HIS E 77 GLN ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 96 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8371 moved from start: 0.2876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13032 Z= 0.203 Angle : 0.617 6.430 18893 Z= 0.368 Chirality : 0.036 0.166 2146 Planarity : 0.004 0.034 1346 Dihedral : 30.292 179.284 4172 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 10.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.38 % Allowed : 14.76 % Favored : 82.86 % 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: 3.08 (0.29), residues: 742 helix: 2.64 (0.21), residues: 538 sheet: None (None), residues: 0 loop : 0.44 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS B 76 PHE 0.011 0.001 PHE A 68 TYR 0.021 0.002 TYR B 99 ARG 0.004 0.000 ARG G 36 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 308 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 293 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 99 TYR cc_start: 0.8699 (m-10) cc_final: 0.8230 (m-80) REVERT: C 74 ASN cc_start: 0.8688 (m-40) cc_final: 0.8380 (t0) REVERT: C 102 THR cc_start: 0.8960 (m) cc_final: 0.8729 (p) REVERT: C 103 ILE cc_start: 0.9178 (mm) cc_final: 0.8937 (mm) REVERT: D 52 ASP cc_start: 0.8406 (p0) cc_final: 0.8033 (p0) REVERT: D 89 THR cc_start: 0.8674 (p) cc_final: 0.8472 (p) REVERT: D 94 GLU cc_start: 0.8371 (mp0) cc_final: 0.7888 (mp0) REVERT: G 105 GLN cc_start: 0.8687 (mp10) cc_final: 0.8292 (mp10) REVERT: G 119 LYS cc_start: 0.8804 (pttt) cc_final: 0.8498 (tppt) REVERT: H 77 GLU cc_start: 0.8300 (mm-30) cc_final: 0.8038 (mm-30) outliers start: 15 outliers final: 6 residues processed: 298 average time/residue: 0.2794 time to fit residues: 113.1952 Evaluate side-chains 252 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 246 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 27 ILE Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 10.0000 chunk 63 optimal weight: 10.0000 chunk 25 optimal weight: 3.9990 chunk 92 optimal weight: 10.0000 chunk 100 optimal weight: 10.0000 chunk 82 optimal weight: 10.0000 chunk 31 optimal weight: 6.9990 chunk 74 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 50 HIS ** E 40 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 32 HIS ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8642 moved from start: 0.4223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.086 13032 Z= 0.459 Angle : 0.709 11.901 18893 Z= 0.407 Chirality : 0.041 0.216 2146 Planarity : 0.005 0.051 1346 Dihedral : 30.692 177.055 4172 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 13.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.94 % Favored : 99.06 % Rotamer: Outliers : 7.30 % Allowed : 16.98 % Favored : 75.71 % 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: 2.95 (0.29), residues: 742 helix: 2.65 (0.21), residues: 538 sheet: None (None), residues: 0 loop : 0.03 (0.36), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 76 PHE 0.012 0.002 PHE D 71 TYR 0.014 0.002 TYR A 100 ARG 0.005 0.001 ARG H 80 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 287 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 241 time to evaluate : 0.916 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8530 (tt0) cc_final: 0.8074 (mt-10) REVERT: A 121 MET cc_start: 0.8381 (mpp) cc_final: 0.8035 (mtt) REVERT: B 24 ARG cc_start: 0.8494 (mtm110) cc_final: 0.8222 (ppt170) REVERT: B 36 ARG cc_start: 0.9283 (mtp85) cc_final: 0.9034 (mtp180) REVERT: C 69 ASN cc_start: 0.9106 (m-40) cc_final: 0.8742 (m-40) REVERT: C 74 ASN cc_start: 0.8841 (m-40) cc_final: 0.8595 (t0) REVERT: D 52 ASP cc_start: 0.8593 (p0) cc_final: 0.8209 (p0) REVERT: D 94 GLU cc_start: 0.8477 (mp0) cc_final: 0.7960 (mp0) REVERT: F 28 GLN cc_start: 0.8564 (pt0) cc_final: 0.7989 (pt0) REVERT: F 85 MET cc_start: 0.8890 (mmm) cc_final: 0.8444 (mmm) REVERT: G 76 LYS cc_start: 0.8764 (mmtt) cc_final: 0.8513 (mmmm) REVERT: G 93 GLU cc_start: 0.8310 (mp0) cc_final: 0.7927 (pm20) REVERT: G 119 LYS cc_start: 0.9047 (pttt) cc_final: 0.8769 (tppt) REVERT: H 114 GLU cc_start: 0.8847 (mm-30) cc_final: 0.8221 (mm-30) REVERT: H 117 LYS cc_start: 0.8940 (mtmm) cc_final: 0.8506 (mttp) outliers start: 46 outliers final: 41 residues processed: 265 average time/residue: 0.2656 time to fit residues: 95.5582 Evaluate side-chains 264 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 223 time to evaluate : 0.965 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 108 THR Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 35 ILE Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 74 THR Chi-restraints excluded: chain C residue 31 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain C residue 60 THR Chi-restraints excluded: chain C residue 101 VAL Chi-restraints excluded: chain D residue 74 ILE Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 81 THR Chi-restraints excluded: chain E residue 108 THR Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain E residue 120 ILE Chi-restraints excluded: chain E residue 131 ILE Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain F residue 87 VAL Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 99 VAL Chi-restraints excluded: chain H residue 119 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 6.9990 chunk 93 optimal weight: 8.9990 chunk 98 optimal weight: 10.0000 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 82 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 74 ASN ** D 85 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.4446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 13032 Z= 0.221 Angle : 0.601 10.461 18893 Z= 0.352 Chirality : 0.034 0.135 2146 Planarity : 0.004 0.038 1346 Dihedral : 30.168 173.091 4172 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 10.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 3.33 % Allowed : 21.75 % Favored : 74.92 % 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: 3.30 (0.30), residues: 742 helix: 2.92 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.13 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 76 PHE 0.013 0.001 PHE D 71 TYR 0.020 0.002 TYR B 99 ARG 0.006 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 277 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 256 time to evaluate : 0.961 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8596 (tt0) cc_final: 0.8148 (mt-10) REVERT: A 80 LYS cc_start: 0.8589 (tppp) cc_final: 0.7405 (ttmm) REVERT: A 121 MET cc_start: 0.8434 (mpp) cc_final: 0.8228 (mtt) REVERT: B 24 ARG cc_start: 0.8641 (mtm110) cc_final: 0.8334 (ppt170) REVERT: B 36 ARG cc_start: 0.9236 (mtp85) cc_final: 0.8842 (mtp-110) REVERT: C 93 GLU cc_start: 0.8903 (mp0) cc_final: 0.8655 (mp0) REVERT: C 113 GLN cc_start: 0.8816 (mp10) cc_final: 0.8567 (mp10) REVERT: D 52 ASP cc_start: 0.8478 (p0) cc_final: 0.7985 (p0) REVERT: D 94 GLU cc_start: 0.8325 (mp0) cc_final: 0.7963 (mp0) REVERT: F 60 LYS cc_start: 0.9036 (tttm) cc_final: 0.8630 (tppt) REVERT: F 85 MET cc_start: 0.8705 (mmm) cc_final: 0.8267 (mmm) REVERT: F 93 ARG cc_start: 0.8658 (ptm-80) cc_final: 0.8429 (ptm160) REVERT: G 69 ASN cc_start: 0.7642 (m110) cc_final: 0.7374 (m110) REVERT: G 119 LYS cc_start: 0.9134 (pttt) cc_final: 0.8889 (tppt) REVERT: H 114 GLU cc_start: 0.8764 (mm-30) cc_final: 0.8047 (mm-30) REVERT: H 117 LYS cc_start: 0.8918 (mtmm) cc_final: 0.8579 (mttp) outliers start: 21 outliers final: 16 residues processed: 263 average time/residue: 0.2748 time to fit residues: 97.2850 Evaluate side-chains 246 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 230 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 110 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 50 VAL Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 9.9990 chunk 73 optimal weight: 10.0000 chunk 40 optimal weight: 8.9990 chunk 84 optimal weight: 10.0000 chunk 68 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 0.9980 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 33 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 2.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN C 74 ASN G 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8550 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 13032 Z= 0.233 Angle : 0.593 8.548 18893 Z= 0.350 Chirality : 0.034 0.140 2146 Planarity : 0.004 0.035 1346 Dihedral : 30.030 175.223 4172 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 11.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.48 % Favored : 98.52 % Rotamer: Outliers : 4.76 % Allowed : 22.22 % Favored : 73.02 % 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: 3.23 (0.30), residues: 742 helix: 2.88 (0.22), residues: 538 sheet: None (None), residues: 0 loop : 0.07 (0.37), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS B 76 PHE 0.011 0.001 PHE D 71 TYR 0.016 0.002 TYR D 84 ARG 0.006 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 240 time to evaluate : 0.829 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 74 GLU cc_start: 0.8657 (tt0) cc_final: 0.8194 (mt-10) REVERT: A 121 MET cc_start: 0.8451 (mpp) cc_final: 0.8154 (mtt) REVERT: B 36 ARG cc_start: 0.9195 (mtp85) cc_final: 0.8828 (mtp-110) REVERT: B 99 TYR cc_start: 0.8713 (m-10) cc_final: 0.8457 (m-80) REVERT: C 74 ASN cc_start: 0.8555 (t160) cc_final: 0.8348 (t0) REVERT: D 52 ASP cc_start: 0.8508 (p0) cc_final: 0.8019 (p0) REVERT: D 94 GLU cc_start: 0.8298 (mp0) cc_final: 0.7956 (mp0) REVERT: F 60 LYS cc_start: 0.8875 (tttm) cc_final: 0.8313 (ttmt) REVERT: F 61 VAL cc_start: 0.9479 (OUTLIER) cc_final: 0.9016 (p) REVERT: F 85 MET cc_start: 0.8748 (mmm) cc_final: 0.8331 (mmm) REVERT: F 93 ARG cc_start: 0.8618 (ptm-80) cc_final: 0.8367 (ptm160) REVERT: G 69 ASN cc_start: 0.7906 (m110) cc_final: 0.7529 (m110) REVERT: G 119 LYS cc_start: 0.9185 (pttt) cc_final: 0.8968 (tppt) outliers start: 30 outliers final: 20 residues processed: 256 average time/residue: 0.2825 time to fit residues: 98.0797 Evaluate side-chains 248 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 227 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 83 LEU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 91 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 98 optimal weight: 10.0000 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 0.0270 chunk 8 optimal weight: 0.4980 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 10.0000 chunk 11 optimal weight: 10.0000 chunk 56 optimal weight: 7.9990 overall best weight: 2.1044 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 94 GLN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13032 Z= 0.228 Angle : 0.608 12.944 18893 Z= 0.355 Chirality : 0.033 0.132 2146 Planarity : 0.004 0.035 1346 Dihedral : 29.957 175.515 4172 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.81 % Favored : 99.19 % Rotamer: Outliers : 5.40 % Allowed : 23.81 % Favored : 70.79 % 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: 3.13 (0.30), residues: 742 helix: 2.77 (0.22), residues: 544 sheet: None (None), residues: 0 loop : 0.05 (0.39), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS F 76 PHE 0.011 0.001 PHE A 79 TYR 0.018 0.002 TYR A 100 ARG 0.006 0.000 ARG D 100 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 272 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 238 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 121 MET cc_start: 0.8452 (mpp) cc_final: 0.8249 (mtt) REVERT: B 36 ARG cc_start: 0.9193 (mtp85) cc_final: 0.8847 (mtp-110) REVERT: B 99 TYR cc_start: 0.8697 (m-10) cc_final: 0.8406 (m-80) REVERT: C 74 ASN cc_start: 0.8627 (t160) cc_final: 0.8382 (t0) REVERT: D 52 ASP cc_start: 0.8515 (p0) cc_final: 0.7996 (p0) REVERT: D 94 GLU cc_start: 0.8281 (mp0) cc_final: 0.7963 (mp0) REVERT: F 60 LYS cc_start: 0.8761 (tttm) cc_final: 0.8495 (ttmt) REVERT: F 61 VAL cc_start: 0.9385 (OUTLIER) cc_final: 0.9163 (p) REVERT: F 85 MET cc_start: 0.8701 (mmm) cc_final: 0.8250 (mmm) REVERT: F 93 ARG cc_start: 0.8634 (ptm-80) cc_final: 0.8403 (ptm160) REVERT: G 69 ASN cc_start: 0.7930 (m110) cc_final: 0.7636 (m110) REVERT: G 119 LYS cc_start: 0.9221 (pttt) cc_final: 0.9014 (tppt) REVERT: H 114 GLU cc_start: 0.8598 (mm-30) cc_final: 0.7861 (mm-30) outliers start: 34 outliers final: 27 residues processed: 253 average time/residue: 0.2693 time to fit residues: 92.6772 Evaluate side-chains 256 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 228 time to evaluate : 0.913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 113 ILE Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 50 LEU Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 55 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 10.0000 chunk 45 optimal weight: 0.8980 chunk 60 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 58 optimal weight: 7.9990 chunk 29 optimal weight: 9.9990 overall best weight: 3.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 74 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.5031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 13032 Z= 0.306 Angle : 0.644 11.112 18893 Z= 0.374 Chirality : 0.036 0.139 2146 Planarity : 0.004 0.036 1346 Dihedral : 30.113 177.300 4172 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 5.87 % Allowed : 22.86 % Favored : 71.27 % 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: 2.89 (0.30), residues: 742 helix: 2.68 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.20 (0.38), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS G 83 PHE 0.017 0.002 PHE D 66 TYR 0.017 0.002 TYR G 51 ARG 0.005 0.001 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 264 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 227 time to evaluate : 0.947 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 36 ARG cc_start: 0.9205 (mtp85) cc_final: 0.8918 (mtp-110) REVERT: C 74 ASN cc_start: 0.8756 (t160) cc_final: 0.8528 (t0) REVERT: D 52 ASP cc_start: 0.8559 (p0) cc_final: 0.8042 (p0) REVERT: D 94 GLU cc_start: 0.8417 (mp0) cc_final: 0.7943 (mp0) REVERT: F 93 ARG cc_start: 0.8766 (ptm-80) cc_final: 0.8492 (ptm160) REVERT: G 69 ASN cc_start: 0.8017 (m110) cc_final: 0.7715 (m110) outliers start: 37 outliers final: 32 residues processed: 245 average time/residue: 0.2813 time to fit residues: 92.5255 Evaluate side-chains 250 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 218 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 74 GLU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 61 VAL Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain D residue 119 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 61 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 ILE Chi-restraints excluded: chain H residue 99 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 66 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 chunk 89 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 5.9990 overall best weight: 1.7962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 94 GLN C 90 ASN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 74 ASN H 85 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.5193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13032 Z= 0.218 Angle : 0.612 10.659 18893 Z= 0.359 Chirality : 0.034 0.148 2146 Planarity : 0.004 0.034 1346 Dihedral : 29.985 177.566 4172 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % Rotamer: Outliers : 5.08 % Allowed : 24.60 % Favored : 70.32 % 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: 2.94 (0.30), residues: 742 helix: 2.69 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.19 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 76 PHE 0.015 0.001 PHE D 66 TYR 0.028 0.002 TYR F 89 ARG 0.005 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 236 time to evaluate : 0.895 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 HIS cc_start: 0.9022 (t-90) cc_final: 0.8804 (t-90) REVERT: A 121 MET cc_start: 0.8460 (mtt) cc_final: 0.8172 (mtt) REVERT: B 36 ARG cc_start: 0.9184 (mtp85) cc_final: 0.8912 (mtp-110) REVERT: C 65 GLU cc_start: 0.8831 (tp30) cc_final: 0.8509 (tp30) REVERT: C 74 ASN cc_start: 0.8716 (t160) cc_final: 0.8469 (t0) REVERT: D 52 ASP cc_start: 0.8516 (p0) cc_final: 0.7971 (p0) REVERT: D 94 GLU cc_start: 0.8288 (mp0) cc_final: 0.7920 (mp0) REVERT: F 93 ARG cc_start: 0.8688 (ptm-80) cc_final: 0.8338 (ptm160) REVERT: G 105 GLN cc_start: 0.8181 (mp10) cc_final: 0.7915 (mp10) outliers start: 32 outliers final: 26 residues processed: 253 average time/residue: 0.2815 time to fit residues: 96.4516 Evaluate side-chains 255 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 229 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 109 ASN Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 31 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 44 VAL Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 28 optimal weight: 4.9990 chunk 82 optimal weight: 10.0000 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 96 optimal weight: 10.0000 chunk 59 optimal weight: 7.9990 chunk 45 optimal weight: 0.6980 chunk 67 optimal weight: 0.9980 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 69 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 85 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8523 moved from start: 0.5288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 13032 Z= 0.226 Angle : 0.633 11.202 18893 Z= 0.365 Chirality : 0.034 0.146 2146 Planarity : 0.004 0.035 1346 Dihedral : 29.961 177.932 4172 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.62 % Favored : 98.38 % Rotamer: Outliers : 4.44 % Allowed : 26.03 % Favored : 69.52 % 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: 2.82 (0.30), residues: 742 helix: 2.60 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.22 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 76 PHE 0.014 0.001 PHE A 79 TYR 0.031 0.002 TYR B 99 ARG 0.007 0.000 ARG D 80 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 257 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 229 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 HIS cc_start: 0.9011 (t-90) cc_final: 0.8807 (t-90) REVERT: A 121 MET cc_start: 0.8430 (mtt) cc_final: 0.7969 (mtt) REVERT: B 36 ARG cc_start: 0.9174 (mtp85) cc_final: 0.8851 (mtp-110) REVERT: C 65 GLU cc_start: 0.8819 (tp30) cc_final: 0.8579 (tp30) REVERT: C 74 ASN cc_start: 0.8732 (t160) cc_final: 0.8474 (t0) REVERT: D 52 ASP cc_start: 0.8465 (p0) cc_final: 0.7934 (p0) REVERT: D 94 GLU cc_start: 0.8289 (mp0) cc_final: 0.7896 (mp0) REVERT: F 93 ARG cc_start: 0.8708 (ptm-80) cc_final: 0.8317 (ptm160) REVERT: G 105 GLN cc_start: 0.8209 (mp10) cc_final: 0.7956 (mp10) outliers start: 28 outliers final: 25 residues processed: 245 average time/residue: 0.2690 time to fit residues: 89.7489 Evaluate side-chains 252 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 227 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 17 THR Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 10.0000 chunk 80 optimal weight: 10.0000 chunk 8 optimal weight: 0.6980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 64 optimal weight: 5.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 74 optimal weight: 10.0000 chunk 11 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 109 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 69 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8529 moved from start: 0.5367 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 13032 Z= 0.241 Angle : 0.639 10.633 18893 Z= 0.369 Chirality : 0.034 0.148 2146 Planarity : 0.004 0.035 1346 Dihedral : 29.981 177.904 4172 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 3.97 % Allowed : 26.67 % Favored : 69.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.73 (0.30), residues: 742 helix: 2.53 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 76 PHE 0.013 0.001 PHE A 79 TYR 0.032 0.003 TYR B 99 ARG 0.008 0.000 ARG D 80 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1484 Ramachandran restraints generated. 742 Oldfield, 0 Emsley, 742 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 233 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 114 HIS cc_start: 0.9060 (t-90) cc_final: 0.8847 (t-90) REVERT: A 121 MET cc_start: 0.8431 (mtt) cc_final: 0.7959 (mtt) REVERT: B 36 ARG cc_start: 0.9177 (mtp85) cc_final: 0.8914 (mtp-110) REVERT: B 89 TYR cc_start: 0.8166 (m-80) cc_final: 0.7722 (m-80) REVERT: C 65 GLU cc_start: 0.8769 (tp30) cc_final: 0.8499 (tp30) REVERT: C 74 ASN cc_start: 0.8803 (t160) cc_final: 0.8539 (t0) REVERT: D 52 ASP cc_start: 0.8438 (p0) cc_final: 0.7918 (p0) REVERT: D 94 GLU cc_start: 0.8348 (mp0) cc_final: 0.7886 (mp0) REVERT: F 93 ARG cc_start: 0.8658 (ptm-80) cc_final: 0.8292 (ptm160) REVERT: G 105 GLN cc_start: 0.8283 (mp10) cc_final: 0.8068 (mp10) outliers start: 25 outliers final: 24 residues processed: 246 average time/residue: 0.2773 time to fit residues: 92.9612 Evaluate side-chains 252 residues out of total 630 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 228 time to evaluate : 0.690 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 VAL Chi-restraints excluded: chain A residue 52 ILE Chi-restraints excluded: chain A residue 58 SER Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 ASP Chi-restraints excluded: chain A residue 95 GLU Chi-restraints excluded: chain A residue 118 VAL Chi-restraints excluded: chain A residue 119 THR Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain C residue 44 VAL Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 58 SER Chi-restraints excluded: chain E residue 110 LEU Chi-restraints excluded: chain E residue 118 VAL Chi-restraints excluded: chain F residue 86 ASP Chi-restraints excluded: chain G residue 35 LEU Chi-restraints excluded: chain G residue 39 ASN Chi-restraints excluded: chain G residue 63 ILE Chi-restraints excluded: chain G residue 86 LEU Chi-restraints excluded: chain G residue 112 ILE Chi-restraints excluded: chain H residue 72 GLU Chi-restraints excluded: chain H residue 90 ILE Chi-restraints excluded: chain H residue 91 THR Chi-restraints excluded: chain H residue 95 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 3.9990 chunk 81 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 83 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 58 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 109 ASN B 76 HIS ** F 26 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.069032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2951 r_free = 0.2951 target = 0.050723 restraints weight = 44935.477| |-----------------------------------------------------------------------------| r_work (start): 0.2907 rms_B_bonded: 2.60 r_work: 0.2732 rms_B_bonded: 4.52 restraints_weight: 0.5000 r_work (final): 0.2732 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.5422 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 13032 Z= 0.284 Angle : 0.656 10.577 18893 Z= 0.378 Chirality : 0.035 0.150 2146 Planarity : 0.004 0.036 1346 Dihedral : 30.081 178.314 4172 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.44 % Allowed : 26.03 % Favored : 69.52 % 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: 2.59 (0.30), residues: 742 helix: 2.45 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS F 76 PHE 0.013 0.001 PHE A 79 TYR 0.034 0.003 TYR F 99 ARG 0.006 0.000 ARG D 80 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2568.33 seconds wall clock time: 46 minutes 35.59 seconds (2795.59 seconds total)