Starting phenix.real_space_refine on Sat Mar 16 17:50:19 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/03_2024/7pey_13361.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/03_2024/7pey_13361.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/03_2024/7pey_13361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/03_2024/7pey_13361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/03_2024/7pey_13361.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/03_2024/7pey_13361.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. 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 342 5.49 5 S 10 5.16 5 C 7159 2.51 5 N 2464 2.21 5 O 3124 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 53": "OE1" <-> "OE2" Residue "M TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M GLU 92": "OE1" <-> "OE2" Residue "N PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 71": "OE1" <-> "OE2" Residue "N GLU 76": "OE1" <-> "OE2" Residue "N GLU 105": "OE1" <-> "OE2" Residue "O PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q PHE 25": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "Q GLU 91": "OE1" <-> "OE2" Residue "R TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 13099 Number of models: 1 Model: "" Number of chains: 10 Chain: "K" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "L" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "M" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "N" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "O" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "P" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "Q" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "R" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3532 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3532 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Chain: "I" Number of atoms: 3479 Number of conformers: 1 Conformer: "" Number of residues, atoms: 171, 3479 Classifications: {'DNA': 171} Link IDs: {'rna3p': 170} Time building chain proxies: 6.62, per 1000 atoms: 0.51 Number of scatterers: 13099 At special positions: 0 Unit cell: (150.15, 130.2, 116.55, 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 10 16.00 P 342 15.00 O 3124 8.00 N 2464 7.00 C 7159 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: 7.68 Conformation dependent library (CDL) restraints added in 1.1 seconds 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1432 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 8 sheets defined 72.0% alpha, 2.1% beta 166 base pairs and 301 stacking pairs defined. Time for finding SS restraints: 6.51 Creating SS restraints... Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.700A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.916A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 4.034A pdb=" N PHE K 78 " --> pdb=" O ILE K 74 " (cutoff:3.500A) Processing helix chain 'K' and resid 85 through 114 Processing helix chain 'K' and resid 120 through 132 removed outlier: 3.819A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 4.055A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N ILE L 29 " --> pdb=" O ILE L 26 " (cutoff:3.500A) Processing helix chain 'L' and resid 30 through 41 Processing helix chain 'L' and resid 50 through 76 Processing helix chain 'L' and resid 82 through 93 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 36 Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.079A pdb=" N VAL M 49 " --> pdb=" O ALA M 45 " (cutoff:3.500A) Processing helix chain 'M' and resid 79 through 89 Processing helix chain 'M' and resid 90 through 97 Processing helix chain 'M' and resid 112 through 116 Processing helix chain 'N' and resid 37 through 49 removed outlier: 3.869A pdb=" N VAL N 41 " --> pdb=" O TYR N 37 " (cutoff:3.500A) Processing helix chain 'N' and resid 55 through 84 Processing helix chain 'N' and resid 90 through 102 removed outlier: 3.531A pdb=" N ILE N 94 " --> pdb=" O THR N 90 " (cutoff:3.500A) Processing helix chain 'N' and resid 103 through 123 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 77 Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 removed outlier: 3.580A pdb=" N ILE O 124 " --> pdb=" O MET O 120 " (cutoff:3.500A) Processing helix chain 'P' and resid 25 through 29 Processing helix chain 'P' and resid 30 through 41 Processing helix chain 'P' and resid 49 through 76 removed outlier: 4.023A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.911A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 removed outlier: 3.503A pdb=" N VAL P 86 " --> pdb=" O THR P 82 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N GLN P 93 " --> pdb=" O ALA P 89 " (cutoff:3.500A) Processing helix chain 'Q' and resid 16 through 22 Processing helix chain 'Q' and resid 26 through 36 Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.238A pdb=" N VAL Q 49 " --> pdb=" O ALA Q 45 " (cutoff:3.500A) Processing helix chain 'Q' and resid 79 through 89 Processing helix chain 'Q' and resid 90 through 97 Processing helix chain 'Q' and resid 112 through 116 Processing helix chain 'R' and resid 37 through 49 Processing helix chain 'R' and resid 55 through 84 Processing helix chain 'R' and resid 90 through 102 Processing helix chain 'R' and resid 104 through 123 removed outlier: 4.156A pdb=" N LYS R 108 " --> pdb=" O GLY R 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 83 through 84 removed outlier: 6.447A pdb=" N ARG K 83 " --> pdb=" O VAL L 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'K' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'L' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'M' and resid 42 through 43 removed outlier: 7.475A pdb=" N ARG M 42 " --> pdb=" O ILE N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'M' and resid 101 through 102 removed outlier: 7.080A pdb=" N THR M 101 " --> pdb=" O TYR P 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.669A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.151A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 400 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 429 hydrogen bonds 858 hydrogen bond angles 0 basepair planarities 166 basepair parallelities 301 stacking parallelities Total time for adding SS restraints: 6.67 Time building geometry restraints manager: 8.09 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2792 1.33 - 1.46: 4997 1.46 - 1.58: 5541 1.58 - 1.70: 682 1.70 - 1.83: 20 Bond restraints: 14032 Sorted by residual: bond pdb=" N GLU O 94 " pdb=" CA GLU O 94 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.20e-02 6.94e+03 6.10e+00 bond pdb=" N LEU O 92 " pdb=" CA LEU O 92 " ideal model delta sigma weight residual 1.459 1.487 -0.028 1.21e-02 6.83e+03 5.47e+00 bond pdb=" N GLN O 93 " pdb=" CA GLN O 93 " ideal model delta sigma weight residual 1.459 1.482 -0.022 1.18e-02 7.18e+03 3.63e+00 bond pdb=" C3' DG I 494 " pdb=" O3' DG I 494 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.59e+00 bond pdb=" C3' DG I 382 " pdb=" O3' DG I 382 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.56e+00 ... (remaining 14027 not shown) Histogram of bond angle deviations from ideal: 97.66 - 104.65: 1371 104.65 - 111.65: 7205 111.65 - 118.64: 4006 118.64 - 125.64: 6720 125.64 - 132.63: 1117 Bond angle restraints: 20419 Sorted by residual: angle pdb=" CB LYS R 46 " pdb=" CG LYS R 46 " pdb=" CD LYS R 46 " ideal model delta sigma weight residual 111.30 122.28 -10.98 2.30e+00 1.89e-01 2.28e+01 angle pdb=" C GLN O 93 " pdb=" CA GLN O 93 " pdb=" CB GLN O 93 " ideal model delta sigma weight residual 110.95 118.24 -7.29 1.55e+00 4.16e-01 2.21e+01 angle pdb=" N GLU K 50 " pdb=" CA GLU K 50 " pdb=" CB GLU K 50 " ideal model delta sigma weight residual 110.40 117.72 -7.32 1.63e+00 3.76e-01 2.02e+01 angle pdb=" N ILE M 79 " pdb=" CA ILE M 79 " pdb=" C ILE M 79 " ideal model delta sigma weight residual 108.45 103.39 5.06 1.20e+00 6.94e-01 1.78e+01 angle pdb=" N LEU O 92 " pdb=" CA LEU O 92 " pdb=" C LEU O 92 " ideal model delta sigma weight residual 111.28 106.73 4.55 1.09e+00 8.42e-01 1.74e+01 ... (remaining 20414 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 36.00: 5768 36.00 - 72.00: 1741 72.00 - 107.99: 22 107.99 - 143.99: 3 143.99 - 179.99: 2 Dihedral angle restraints: 7536 sinusoidal: 5314 harmonic: 2222 Sorted by residual: dihedral pdb=" CA ILE L 50 " pdb=" C ILE L 50 " pdb=" N TYR L 51 " pdb=" CA TYR L 51 " ideal model delta harmonic sigma weight residual 180.00 -156.36 -23.64 0 5.00e+00 4.00e-02 2.23e+01 dihedral pdb=" CA PRO N 103 " pdb=" C PRO N 103 " pdb=" N GLY N 104 " pdb=" CA GLY N 104 " ideal model delta harmonic sigma weight residual 180.00 157.20 22.80 0 5.00e+00 4.00e-02 2.08e+01 dihedral pdb=" CA ASP N 51 " pdb=" C ASP N 51 " pdb=" N THR N 52 " pdb=" CA THR N 52 " ideal model delta harmonic sigma weight residual 180.00 -159.05 -20.95 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 7533 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1730 0.049 - 0.098: 486 0.098 - 0.148: 90 0.148 - 0.197: 8 0.197 - 0.246: 6 Chirality restraints: 2320 Sorted by residual: chirality pdb=" CG LEU M 23 " pdb=" CB LEU M 23 " pdb=" CD1 LEU M 23 " pdb=" CD2 LEU M 23 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.51e+00 chirality pdb=" CA LEU O 92 " pdb=" N LEU O 92 " pdb=" C LEU O 92 " pdb=" CB LEU O 92 " both_signs ideal model delta sigma weight residual False 2.51 2.74 -0.23 2.00e-01 2.50e+01 1.29e+00 chirality pdb=" CB VAL O 101 " pdb=" CA VAL O 101 " pdb=" CG1 VAL O 101 " pdb=" CG2 VAL O 101 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 ... (remaining 2317 not shown) Planarity restraints: 1398 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB HIS L 75 " -0.035 2.00e-02 2.50e+03 2.80e-02 1.18e+01 pdb=" CG HIS L 75 " 0.052 2.00e-02 2.50e+03 pdb=" ND1 HIS L 75 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 HIS L 75 " -0.002 2.00e-02 2.50e+03 pdb=" CE1 HIS L 75 " -0.024 2.00e-02 2.50e+03 pdb=" NE2 HIS L 75 " -0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR R 83 " -0.027 2.00e-02 2.50e+03 2.18e-02 9.48e+00 pdb=" CG TYR R 83 " 0.053 2.00e-02 2.50e+03 pdb=" CD1 TYR R 83 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 TYR R 83 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR R 83 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR R 83 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR R 83 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR R 83 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE P 100 " -0.014 2.00e-02 2.50e+03 2.22e-02 8.60e+00 pdb=" CG PHE P 100 " 0.050 2.00e-02 2.50e+03 pdb=" CD1 PHE P 100 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE P 100 " -0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE P 100 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE P 100 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE P 100 " 0.000 2.00e-02 2.50e+03 ... (remaining 1395 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 1084 2.72 - 3.27: 11922 3.27 - 3.81: 28286 3.81 - 4.36: 32152 4.36 - 4.90: 44433 Nonbonded interactions: 117877 Sorted by model distance: nonbonded pdb=" OH TYR Q 39 " pdb=" OE1 GLU R 71 " model vdw 2.177 2.440 nonbonded pdb=" OG SER M 40 " pdb=" O ARG M 42 " model vdw 2.197 2.440 nonbonded pdb=" O LEU O 61 " pdb=" NH2 ARG P 36 " model vdw 2.283 2.520 nonbonded pdb=" OD2 ASP K 106 " pdb=" NH2 ARG K 131 " model vdw 2.288 2.520 nonbonded pdb=" O LEU M 85 " pdb=" ND2 ASN M 89 " model vdw 2.291 2.520 ... (remaining 117872 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 'K' selection = chain 'O' } ncs_group { reference = chain 'L' selection = chain 'P' } ncs_group { reference = chain 'M' selection = chain 'Q' } ncs_group { reference = chain 'N' selection = chain 'R' } 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 group one per residue 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: 1.690 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.090 Construct map_model_manager: 0.010 Extract box with map and model: 6.080 Check model and map are aligned: 0.150 Set scattering table: 0.110 Process input model: 44.410 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.850 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 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 : 0.006 0.057 14032 Z= 0.333 Angle : 0.895 11.536 20419 Z= 0.510 Chirality : 0.047 0.246 2320 Planarity : 0.007 0.062 1398 Dihedral : 29.812 179.988 6104 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.00 % Allowed : 0.47 % Favored : 99.53 % 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 (0.28), residues: 752 helix: 0.19 (0.21), residues: 536 sheet: None (None), residues: 0 loop : -0.36 (0.37), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.017 0.002 HIS L 75 PHE 0.050 0.003 PHE P 100 TYR 0.053 0.003 TYR R 83 ARG 0.015 0.001 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 176 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 50 GLU cc_start: 0.9460 (pm20) cc_final: 0.9031 (pm20) REVERT: K 85 GLN cc_start: 0.9086 (mt0) cc_final: 0.8802 (mt0) REVERT: K 90 MET cc_start: 0.9440 (mmp) cc_final: 0.9203 (mmp) REVERT: K 120 MET cc_start: 0.8702 (mtm) cc_final: 0.8213 (mtt) REVERT: L 75 HIS cc_start: 0.9443 (t70) cc_final: 0.8943 (t70) REVERT: M 36 LYS cc_start: 0.9401 (mppt) cc_final: 0.9053 (mmtm) REVERT: M 64 GLU cc_start: 0.9578 (mm-30) cc_final: 0.9301 (mm-30) REVERT: M 79 ILE cc_start: 0.9590 (tp) cc_final: 0.9318 (pt) REVERT: N 96 THR cc_start: 0.9683 (m) cc_final: 0.9463 (m) REVERT: N 99 ARG cc_start: 0.9334 (mtp85) cc_final: 0.8543 (ttm110) REVERT: N 102 LEU cc_start: 0.8854 (tp) cc_final: 0.8421 (tt) REVERT: O 86 SER cc_start: 0.9826 (t) cc_final: 0.9545 (t) REVERT: O 90 MET cc_start: 0.9660 (mmp) cc_final: 0.9173 (mmm) REVERT: O 120 MET cc_start: 0.8299 (mtt) cc_final: 0.8035 (mtt) REVERT: O 125 GLN cc_start: 0.9400 (mt0) cc_final: 0.9195 (mt0) REVERT: P 72 TYR cc_start: 0.9560 (m-80) cc_final: 0.9259 (m-80) REVERT: Q 87 ILE cc_start: 0.9480 (mm) cc_final: 0.9159 (mm) REVERT: Q 90 ASP cc_start: 0.8905 (t70) cc_final: 0.8392 (t0) REVERT: R 93 GLU cc_start: 0.9067 (mp0) cc_final: 0.8802 (mp0) REVERT: R 113 GLU cc_start: 0.9357 (mm-30) cc_final: 0.9000 (mm-30) outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2634 time to fit residues: 65.3097 Evaluate side-chains 116 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.945 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 89 optimal weight: 10.0000 chunk 80 optimal weight: 5.9990 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 20.0000 chunk 54 optimal weight: 0.1980 chunk 42 optimal weight: 0.9990 chunk 83 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 50 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14032 Z= 0.217 Angle : 0.608 5.812 20419 Z= 0.366 Chirality : 0.034 0.124 2320 Planarity : 0.005 0.058 1398 Dihedral : 32.314 179.508 4580 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 0.63 % Allowed : 2.67 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.30), residues: 752 helix: 1.35 (0.22), residues: 540 sheet: None (None), residues: 0 loop : 0.09 (0.40), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 75 PHE 0.025 0.002 PHE O 104 TYR 0.019 0.002 TYR R 83 ARG 0.014 0.000 ARG M 42 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 150 time to evaluate : 1.066 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9395 (m-80) cc_final: 0.8872 (m-80) REVERT: K 85 GLN cc_start: 0.9202 (mt0) cc_final: 0.8887 (mt0) REVERT: K 90 MET cc_start: 0.9301 (mmp) cc_final: 0.8949 (mmp) REVERT: K 94 GLU cc_start: 0.9531 (mm-30) cc_final: 0.9229 (mm-30) REVERT: K 120 MET cc_start: 0.8696 (mtm) cc_final: 0.8254 (mtt) REVERT: M 36 LYS cc_start: 0.9262 (mppt) cc_final: 0.8835 (mmtm) REVERT: M 38 ASN cc_start: 0.8478 (OUTLIER) cc_final: 0.7967 (t0) REVERT: M 64 GLU cc_start: 0.9587 (mm-30) cc_final: 0.9381 (mm-30) REVERT: N 45 LEU cc_start: 0.9314 (pp) cc_final: 0.8975 (pp) REVERT: N 71 GLU cc_start: 0.9040 (mm-30) cc_final: 0.8665 (mm-30) REVERT: N 102 LEU cc_start: 0.8588 (tp) cc_final: 0.8330 (tp) REVERT: O 86 SER cc_start: 0.9804 (t) cc_final: 0.9578 (t) REVERT: O 104 PHE cc_start: 0.9061 (m-80) cc_final: 0.8611 (m-80) REVERT: O 120 MET cc_start: 0.8281 (mtt) cc_final: 0.7934 (mtt) REVERT: R 76 GLU cc_start: 0.9302 (tp30) cc_final: 0.8873 (mt-10) REVERT: R 83 TYR cc_start: 0.8846 (m-10) cc_final: 0.8528 (m-80) REVERT: R 101 LEU cc_start: 0.9503 (tt) cc_final: 0.9092 (tt) REVERT: R 113 GLU cc_start: 0.9401 (mm-30) cc_final: 0.9075 (mm-30) outliers start: 4 outliers final: 2 residues processed: 152 average time/residue: 0.2208 time to fit residues: 50.3743 Evaluate side-chains 104 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 101 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 65 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 96 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 85 optimal weight: 7.9990 chunk 95 optimal weight: 5.9990 chunk 32 optimal weight: 9.9990 chunk 77 optimal weight: 6.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 109 HIS ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.3733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.050 14032 Z= 0.472 Angle : 0.776 9.846 20419 Z= 0.455 Chirality : 0.042 0.200 2320 Planarity : 0.006 0.071 1398 Dihedral : 33.280 172.297 4580 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 29.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 4.56 % Favored : 95.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.28), residues: 752 helix: 0.99 (0.22), residues: 536 sheet: None (None), residues: 0 loop : -0.29 (0.36), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.012 0.002 HIS P 75 PHE 0.023 0.003 PHE K 104 TYR 0.020 0.002 TYR N 40 ARG 0.010 0.001 ARG Q 42 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9524 (m-80) cc_final: 0.9084 (m-80) REVERT: K 85 GLN cc_start: 0.9196 (mt0) cc_final: 0.8621 (mt0) REVERT: K 90 MET cc_start: 0.9313 (mmp) cc_final: 0.8961 (mmp) REVERT: K 94 GLU cc_start: 0.9575 (mm-30) cc_final: 0.9323 (mm-30) REVERT: K 104 PHE cc_start: 0.9544 (m-80) cc_final: 0.9333 (m-10) REVERT: K 120 MET cc_start: 0.8563 (mtm) cc_final: 0.8053 (mtt) REVERT: L 75 HIS cc_start: 0.9501 (t70) cc_final: 0.9270 (t70) REVERT: M 41 GLU cc_start: 0.9302 (mp0) cc_final: 0.8259 (tp30) REVERT: N 102 LEU cc_start: 0.8696 (tp) cc_final: 0.8373 (tp) REVERT: N 109 HIS cc_start: 0.9740 (m90) cc_final: 0.9440 (m170) REVERT: O 86 SER cc_start: 0.9808 (t) cc_final: 0.9491 (p) REVERT: O 94 GLU cc_start: 0.9479 (mp0) cc_final: 0.9262 (mp0) REVERT: O 104 PHE cc_start: 0.9448 (m-80) cc_final: 0.9005 (m-80) REVERT: O 120 MET cc_start: 0.7873 (mtt) cc_final: 0.7452 (mtt) REVERT: R 62 MET cc_start: 0.9311 (mmp) cc_final: 0.9074 (mmp) REVERT: R 113 GLU cc_start: 0.9396 (mm-30) cc_final: 0.9076 (mm-30) outliers start: 0 outliers final: 0 residues processed: 117 average time/residue: 0.2275 time to fit residues: 39.8361 Evaluate side-chains 90 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 4.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 5.9990 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 5.9990 chunk 27 optimal weight: 8.9990 chunk 85 optimal weight: 3.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Q 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.3754 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 14032 Z= 0.247 Angle : 0.624 6.929 20419 Z= 0.375 Chirality : 0.035 0.167 2320 Planarity : 0.004 0.057 1398 Dihedral : 33.006 178.195 4580 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 17.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.16 % Allowed : 3.14 % Favored : 96.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.48 (0.30), residues: 752 helix: 1.46 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.14 (0.39), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 75 PHE 0.017 0.002 PHE K 104 TYR 0.031 0.002 TYR R 83 ARG 0.006 0.000 ARG Q 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9543 (m-80) cc_final: 0.9123 (m-80) REVERT: K 85 GLN cc_start: 0.9105 (mt0) cc_final: 0.8611 (mt0) REVERT: K 90 MET cc_start: 0.9337 (mmp) cc_final: 0.8877 (mmp) REVERT: K 94 GLU cc_start: 0.9487 (mm-30) cc_final: 0.9254 (mm-30) REVERT: K 120 MET cc_start: 0.8671 (mtm) cc_final: 0.8008 (mtt) REVERT: L 63 GLU cc_start: 0.9313 (mt-10) cc_final: 0.9085 (mt-10) REVERT: L 75 HIS cc_start: 0.9476 (t70) cc_final: 0.9232 (t70) REVERT: M 41 GLU cc_start: 0.9275 (mp0) cc_final: 0.8285 (tp30) REVERT: N 102 LEU cc_start: 0.8710 (tp) cc_final: 0.8371 (tp) REVERT: N 105 GLU cc_start: 0.8976 (pm20) cc_final: 0.8435 (pm20) REVERT: N 109 HIS cc_start: 0.9701 (m90) cc_final: 0.9346 (m-70) REVERT: O 100 LEU cc_start: 0.9731 (mt) cc_final: 0.9525 (mt) REVERT: O 104 PHE cc_start: 0.9402 (m-80) cc_final: 0.8992 (m-80) REVERT: O 106 ASP cc_start: 0.9371 (m-30) cc_final: 0.9150 (m-30) REVERT: O 120 MET cc_start: 0.7971 (mtt) cc_final: 0.7503 (mtt) REVERT: R 113 GLU cc_start: 0.9400 (mm-30) cc_final: 0.9067 (mm-30) outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.2243 time to fit residues: 44.5665 Evaluate side-chains 99 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 98 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 58 optimal weight: 0.7980 chunk 1 optimal weight: 7.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 5.9990 chunk 87 optimal weight: 7.9990 chunk 70 optimal weight: 9.9990 chunk 0 optimal weight: 10.0000 chunk 52 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 chunk 34 optimal weight: 4.9990 overall best weight: 4.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 55 GLN K 93 GLN ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 14032 Z= 0.348 Angle : 0.679 7.090 20419 Z= 0.404 Chirality : 0.037 0.179 2320 Planarity : 0.005 0.060 1398 Dihedral : 33.116 178.236 4580 Min Nonbonded Distance : 2.077 Molprobity Statistics. All-atom Clashscore : 23.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 0.16 % Allowed : 3.30 % Favored : 96.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.21 (0.30), residues: 752 helix: 1.30 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.38 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS P 75 PHE 0.025 0.002 PHE K 104 TYR 0.024 0.002 TYR R 83 ARG 0.005 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 129 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9540 (m-80) cc_final: 0.9130 (m-80) REVERT: K 90 MET cc_start: 0.9351 (mmp) cc_final: 0.8967 (mmp) REVERT: K 94 GLU cc_start: 0.9618 (mm-30) cc_final: 0.9304 (mm-30) REVERT: K 120 MET cc_start: 0.8567 (mtm) cc_final: 0.7932 (mtt) REVERT: L 75 HIS cc_start: 0.9482 (t70) cc_final: 0.9216 (t70) REVERT: M 36 LYS cc_start: 0.9366 (mptt) cc_final: 0.9064 (mmtm) REVERT: M 41 GLU cc_start: 0.9148 (mp0) cc_final: 0.8417 (tp30) REVERT: N 59 MET cc_start: 0.9110 (tpp) cc_final: 0.8901 (tpt) REVERT: N 102 LEU cc_start: 0.8699 (tp) cc_final: 0.8329 (tp) REVERT: N 109 HIS cc_start: 0.9604 (m90) cc_final: 0.9321 (m-70) REVERT: O 67 PHE cc_start: 0.8941 (t80) cc_final: 0.8709 (t80) REVERT: O 93 GLN cc_start: 0.9451 (pt0) cc_final: 0.9239 (pt0) REVERT: O 104 PHE cc_start: 0.9464 (m-80) cc_final: 0.8988 (m-80) REVERT: O 120 MET cc_start: 0.8064 (mtt) cc_final: 0.7585 (mtt) REVERT: R 113 GLU cc_start: 0.9404 (mm-30) cc_final: 0.9090 (mm-30) outliers start: 1 outliers final: 1 residues processed: 130 average time/residue: 0.2180 time to fit residues: 42.8569 Evaluate side-chains 98 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 97 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 5.9990 chunk 20 optimal weight: 6.9990 chunk 60 optimal weight: 0.9990 chunk 25 optimal weight: 4.9990 chunk 102 optimal weight: 7.9990 chunk 85 optimal weight: 5.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 chunk 53 optimal weight: 10.0000 chunk 98 optimal weight: 7.9990 overall best weight: 2.8788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.4751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 14032 Z= 0.256 Angle : 0.624 6.654 20419 Z= 0.375 Chirality : 0.035 0.162 2320 Planarity : 0.004 0.061 1398 Dihedral : 32.922 177.942 4580 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 18.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.16 % Allowed : 1.89 % Favored : 97.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.30), residues: 752 helix: 1.53 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.37 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 39 PHE 0.027 0.002 PHE K 104 TYR 0.038 0.002 TYR R 83 ARG 0.003 0.000 ARG L 45 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 0.948 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9546 (m-10) cc_final: 0.9048 (m-80) REVERT: K 85 GLN cc_start: 0.9311 (mt0) cc_final: 0.8853 (mt0) REVERT: K 90 MET cc_start: 0.9133 (mmp) cc_final: 0.8799 (mmp) REVERT: K 94 GLU cc_start: 0.9528 (mm-30) cc_final: 0.9196 (mm-30) REVERT: K 120 MET cc_start: 0.8746 (mtm) cc_final: 0.7915 (mtt) REVERT: L 75 HIS cc_start: 0.9502 (t70) cc_final: 0.9178 (t70) REVERT: M 36 LYS cc_start: 0.9470 (mptt) cc_final: 0.9200 (mmtm) REVERT: M 41 GLU cc_start: 0.9073 (mp0) cc_final: 0.8431 (tp30) REVERT: N 102 LEU cc_start: 0.8751 (tp) cc_final: 0.8343 (tp) REVERT: N 105 GLU cc_start: 0.9607 (mp0) cc_final: 0.9286 (pm20) REVERT: N 109 HIS cc_start: 0.9602 (m90) cc_final: 0.9230 (m-70) REVERT: O 67 PHE cc_start: 0.8961 (t80) cc_final: 0.8741 (t80) REVERT: O 93 GLN cc_start: 0.9435 (pt0) cc_final: 0.9107 (pt0) REVERT: O 104 PHE cc_start: 0.9435 (m-80) cc_final: 0.8878 (m-80) REVERT: O 120 MET cc_start: 0.8103 (mtt) cc_final: 0.7653 (mtt) REVERT: Q 36 LYS cc_start: 0.9440 (mmtm) cc_final: 0.9070 (mmtm) REVERT: R 113 GLU cc_start: 0.9416 (mm-30) cc_final: 0.9082 (mm-30) outliers start: 1 outliers final: 0 residues processed: 139 average time/residue: 0.2705 time to fit residues: 55.1521 Evaluate side-chains 105 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 11 optimal weight: 10.0000 chunk 58 optimal weight: 2.9990 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 8.9990 chunk 63 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 47 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8495 moved from start: 0.4966 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14032 Z= 0.231 Angle : 0.615 6.637 20419 Z= 0.369 Chirality : 0.035 0.161 2320 Planarity : 0.004 0.061 1398 Dihedral : 32.723 178.389 4580 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 17.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.30), residues: 752 helix: 1.59 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.17 (0.40), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 39 PHE 0.021 0.002 PHE K 67 TYR 0.028 0.002 TYR R 83 ARG 0.003 0.000 ARG P 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 139 time to evaluate : 1.085 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9539 (m-10) cc_final: 0.9020 (m-80) REVERT: K 85 GLN cc_start: 0.9315 (mt0) cc_final: 0.8856 (mt0) REVERT: K 90 MET cc_start: 0.9140 (mmp) cc_final: 0.8788 (mmp) REVERT: K 94 GLU cc_start: 0.9513 (mm-30) cc_final: 0.9180 (mm-30) REVERT: K 120 MET cc_start: 0.8727 (mtm) cc_final: 0.7944 (mtt) REVERT: L 63 GLU cc_start: 0.9311 (mt-10) cc_final: 0.9057 (mt-10) REVERT: L 75 HIS cc_start: 0.9507 (t70) cc_final: 0.9181 (t70) REVERT: M 36 LYS cc_start: 0.9485 (mptt) cc_final: 0.9223 (mmtm) REVERT: M 41 GLU cc_start: 0.9022 (mp0) cc_final: 0.8445 (tp30) REVERT: M 56 GLU cc_start: 0.9162 (mt-10) cc_final: 0.8934 (mt-10) REVERT: M 79 ILE cc_start: 0.9521 (tp) cc_final: 0.9221 (pt) REVERT: N 59 MET cc_start: 0.9064 (tpp) cc_final: 0.8846 (tpt) REVERT: N 102 LEU cc_start: 0.8612 (tp) cc_final: 0.8275 (tp) REVERT: N 109 HIS cc_start: 0.9610 (m90) cc_final: 0.9279 (m-70) REVERT: O 104 PHE cc_start: 0.9375 (m-80) cc_final: 0.8763 (m-80) REVERT: O 120 MET cc_start: 0.8135 (mtt) cc_final: 0.7701 (mtt) REVERT: P 91 LYS cc_start: 0.9485 (tmmt) cc_final: 0.9017 (pttm) REVERT: Q 36 LYS cc_start: 0.9415 (mmtm) cc_final: 0.9010 (mmtm) REVERT: R 113 GLU cc_start: 0.9426 (mm-30) cc_final: 0.9079 (mm-30) outliers start: 0 outliers final: 0 residues processed: 139 average time/residue: 0.2437 time to fit residues: 49.0748 Evaluate side-chains 107 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.961 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 30 optimal weight: 0.9990 chunk 20 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 64 optimal weight: 0.7980 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 89 optimal weight: 10.0000 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN P 27 GLN Q 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.5119 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14032 Z= 0.177 Angle : 0.596 7.206 20419 Z= 0.356 Chirality : 0.035 0.197 2320 Planarity : 0.004 0.062 1398 Dihedral : 32.351 179.806 4580 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 0.16 % Allowed : 1.42 % Favored : 98.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.31), residues: 752 helix: 1.89 (0.23), residues: 532 sheet: None (None), residues: 0 loop : -0.26 (0.40), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 39 PHE 0.021 0.002 PHE R 65 TYR 0.024 0.002 TYR P 72 ARG 0.003 0.000 ARG M 20 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.958 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9460 (m-10) cc_final: 0.8960 (m-80) REVERT: K 77 ASP cc_start: 0.9564 (t70) cc_final: 0.9278 (m-30) REVERT: K 85 GLN cc_start: 0.9234 (mt0) cc_final: 0.8914 (mt0) REVERT: K 90 MET cc_start: 0.9136 (mmp) cc_final: 0.8753 (mmp) REVERT: K 94 GLU cc_start: 0.9468 (mm-30) cc_final: 0.9092 (mm-30) REVERT: K 120 MET cc_start: 0.8648 (mtm) cc_final: 0.7796 (mtt) REVERT: L 75 HIS cc_start: 0.9479 (t70) cc_final: 0.9175 (t70) REVERT: M 36 LYS cc_start: 0.9516 (mptt) cc_final: 0.9248 (mmtm) REVERT: M 41 GLU cc_start: 0.9066 (mp0) cc_final: 0.8493 (tp30) REVERT: M 79 ILE cc_start: 0.9559 (tp) cc_final: 0.9277 (pt) REVERT: N 102 LEU cc_start: 0.8612 (tp) cc_final: 0.8305 (tp) REVERT: N 105 GLU cc_start: 0.9055 (pm20) cc_final: 0.8753 (pm20) REVERT: N 109 HIS cc_start: 0.9649 (m90) cc_final: 0.9304 (m170) REVERT: O 86 SER cc_start: 0.9773 (p) cc_final: 0.9469 (p) REVERT: O 104 PHE cc_start: 0.9277 (m-80) cc_final: 0.8732 (m-80) REVERT: O 120 MET cc_start: 0.8217 (mtt) cc_final: 0.7778 (mtt) REVERT: P 58 LEU cc_start: 0.9810 (tt) cc_final: 0.9514 (pp) REVERT: P 91 LYS cc_start: 0.9449 (tmmt) cc_final: 0.9041 (pttm) REVERT: Q 36 LYS cc_start: 0.9420 (mmtm) cc_final: 0.9000 (mmtm) REVERT: Q 38 ASN cc_start: 0.8350 (OUTLIER) cc_final: 0.7903 (p0) REVERT: R 83 TYR cc_start: 0.8685 (m-80) cc_final: 0.8289 (m-80) REVERT: R 113 GLU cc_start: 0.9415 (mm-30) cc_final: 0.9069 (mm-30) outliers start: 1 outliers final: 0 residues processed: 149 average time/residue: 0.2327 time to fit residues: 51.4139 Evaluate side-chains 110 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 109 time to evaluate : 0.976 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 6.9990 chunk 97 optimal weight: 7.9990 chunk 57 optimal weight: 1.9990 chunk 41 optimal weight: 9.9990 chunk 74 optimal weight: 8.9990 chunk 29 optimal weight: 0.0980 chunk 86 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 8.9990 chunk 62 optimal weight: 10.0000 chunk 100 optimal weight: 8.9990 overall best weight: 5.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 73 ASN ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.5602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.074 14032 Z= 0.387 Angle : 0.704 7.597 20419 Z= 0.417 Chirality : 0.039 0.200 2320 Planarity : 0.005 0.058 1398 Dihedral : 32.876 176.512 4580 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 25.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % 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: 1.28 (0.30), residues: 752 helix: 1.34 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.32 (0.41), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS O 39 PHE 0.018 0.003 PHE K 67 TYR 0.019 0.002 TYR N 40 ARG 0.005 0.001 ARG P 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 128 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9483 (m-10) cc_final: 0.8913 (m-80) REVERT: K 85 GLN cc_start: 0.9327 (mt0) cc_final: 0.8965 (mt0) REVERT: K 90 MET cc_start: 0.9134 (mmp) cc_final: 0.8863 (mmp) REVERT: K 94 GLU cc_start: 0.9591 (mm-30) cc_final: 0.9256 (mm-30) REVERT: K 120 MET cc_start: 0.8637 (mtm) cc_final: 0.7976 (mtt) REVERT: L 63 GLU cc_start: 0.9314 (mt-10) cc_final: 0.9107 (mt-10) REVERT: L 75 HIS cc_start: 0.9499 (t70) cc_final: 0.9101 (t70) REVERT: L 91 LYS cc_start: 0.9532 (tmmt) cc_final: 0.9219 (pttm) REVERT: M 36 LYS cc_start: 0.9437 (mptt) cc_final: 0.9193 (mmtm) REVERT: M 41 GLU cc_start: 0.8985 (mp0) cc_final: 0.8531 (tp30) REVERT: N 59 MET cc_start: 0.9049 (tpp) cc_final: 0.8844 (tpt) REVERT: N 102 LEU cc_start: 0.8780 (tp) cc_final: 0.8417 (tp) REVERT: N 105 GLU cc_start: 0.9130 (pm20) cc_final: 0.8840 (pm20) REVERT: N 109 HIS cc_start: 0.9660 (m90) cc_final: 0.9387 (m-70) REVERT: O 104 PHE cc_start: 0.9466 (m-80) cc_final: 0.8924 (m-80) REVERT: O 120 MET cc_start: 0.8105 (mtt) cc_final: 0.7643 (mtt) REVERT: P 91 LYS cc_start: 0.9488 (tmmt) cc_final: 0.9133 (pttm) REVERT: R 113 GLU cc_start: 0.9424 (mm-30) cc_final: 0.9044 (mm-30) outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2186 time to fit residues: 41.9801 Evaluate side-chains 95 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 61 optimal weight: 0.6980 chunk 47 optimal weight: 10.0000 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 6.9990 chunk 84 optimal weight: 5.9990 chunk 8 optimal weight: 0.8980 chunk 64 optimal weight: 0.9980 chunk 51 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8461 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 : 0.003 0.036 14032 Z= 0.191 Angle : 0.617 8.514 20419 Z= 0.367 Chirality : 0.036 0.219 2320 Planarity : 0.004 0.062 1398 Dihedral : 32.462 179.363 4580 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 16.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.00 % Allowed : 0.31 % Favored : 99.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.30), residues: 752 helix: 1.60 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.28 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS O 39 PHE 0.019 0.002 PHE R 65 TYR 0.019 0.002 TYR M 50 ARG 0.003 0.000 ARG N 31 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1504 Ramachandran restraints generated. 752 Oldfield, 0 Emsley, 752 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.9420 (m-10) cc_final: 0.8933 (m-80) REVERT: K 85 GLN cc_start: 0.9246 (mt0) cc_final: 0.8846 (mt0) REVERT: K 90 MET cc_start: 0.9173 (mmp) cc_final: 0.8790 (mmp) REVERT: K 94 GLU cc_start: 0.9475 (mm-30) cc_final: 0.9138 (mm-30) REVERT: K 120 MET cc_start: 0.8578 (mtm) cc_final: 0.7800 (mtt) REVERT: L 58 LEU cc_start: 0.9756 (tt) cc_final: 0.9544 (pp) REVERT: L 63 GLU cc_start: 0.9272 (mt-10) cc_final: 0.9061 (mt-10) REVERT: L 75 HIS cc_start: 0.9446 (t70) cc_final: 0.9096 (t70) REVERT: L 91 LYS cc_start: 0.9496 (tmmt) cc_final: 0.9154 (pttm) REVERT: M 25 PHE cc_start: 0.7456 (m-80) cc_final: 0.7220 (m-80) REVERT: M 26 PRO cc_start: 0.8605 (Cg_endo) cc_final: 0.8370 (Cg_exo) REVERT: M 36 LYS cc_start: 0.9516 (mptt) cc_final: 0.9222 (mmtm) REVERT: M 41 GLU cc_start: 0.8966 (mp0) cc_final: 0.8522 (tp30) REVERT: M 79 ILE cc_start: 0.9555 (tp) cc_final: 0.9272 (pt) REVERT: N 102 LEU cc_start: 0.8667 (tp) cc_final: 0.8304 (tp) REVERT: N 105 GLU cc_start: 0.9160 (pm20) cc_final: 0.8799 (pm20) REVERT: N 109 HIS cc_start: 0.9696 (m90) cc_final: 0.9426 (m170) REVERT: O 86 SER cc_start: 0.9787 (p) cc_final: 0.9506 (p) REVERT: O 90 MET cc_start: 0.9745 (mpp) cc_final: 0.9419 (mpp) REVERT: O 93 GLN cc_start: 0.9629 (pt0) cc_final: 0.9412 (pt0) REVERT: O 104 PHE cc_start: 0.9396 (m-80) cc_final: 0.8889 (m-80) REVERT: O 120 MET cc_start: 0.8258 (mtt) cc_final: 0.7845 (mtt) REVERT: P 91 LYS cc_start: 0.9462 (tmmt) cc_final: 0.9079 (pttm) REVERT: Q 25 PHE cc_start: 0.8666 (m-10) cc_final: 0.8433 (m-80) REVERT: Q 36 LYS cc_start: 0.9389 (mptt) cc_final: 0.9154 (mmtm) REVERT: R 83 TYR cc_start: 0.8751 (m-80) cc_final: 0.8374 (m-80) REVERT: R 102 LEU cc_start: 0.9433 (tp) cc_final: 0.9227 (tt) REVERT: R 113 GLU cc_start: 0.9428 (mm-30) cc_final: 0.9063 (mm-30) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.2347 time to fit residues: 48.3867 Evaluate side-chains 112 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 112 time to evaluate : 0.925 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 25 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 12 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 8.9990 chunk 73 optimal weight: 8.9990 chunk 4 optimal weight: 0.9980 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2837 r_free = 0.2837 target = 0.027595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.020586 restraints weight = 179872.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.021346 restraints weight = 87758.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.2595 r_free = 0.2595 target = 0.021864 restraints weight = 53789.507| |-----------------------------------------------------------------------------| r_work (final): 0.2583 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8538 moved from start: 0.5784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 14032 Z= 0.284 Angle : 0.644 7.497 20419 Z= 0.383 Chirality : 0.037 0.369 2320 Planarity : 0.004 0.057 1398 Dihedral : 32.659 177.798 4580 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 20.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % 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: 1.54 (0.30), residues: 752 helix: 1.55 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.27 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS O 39 PHE 0.029 0.003 PHE K 104 TYR 0.024 0.002 TYR M 50 ARG 0.008 0.000 ARG M 20 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1962.80 seconds wall clock time: 36 minutes 34.87 seconds (2194.87 seconds total)