Starting phenix.real_space_refine (version: 1.21rc1) on Fri Jul 7 20:21:49 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/07_2023/7pey_13361.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/07_2023/7pey_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_13361/07_2023/7pey_13361.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/07_2023/7pey_13361.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/07_2023/7pey_13361.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pey_13361/07_2023/7pey_13361.pdb" } resolution = 4.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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-1.21rc1-5013/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: 5.98, per 1000 atoms: 0.46 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: 7.27 Conformation dependent library (CDL) restraints added in 932.8 milliseconds 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: 5.90 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: 6.32 Time building geometry restraints manager: 7.56 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: 5519 36.00 - 72.00: 1702 72.00 - 107.99: 22 107.99 - 143.99: 3 143.99 - 179.99: 2 Dihedral angle restraints: 7248 sinusoidal: 5026 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 7245 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: 1.710 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.010 Extract box with map and model: 6.660 Check model and map are aligned: 0.200 Set scattering table: 0.120 Process input model: 41.470 Find NCS groups from input model: 0.460 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: 0.000 Load rotamer database and sin/cos tables:2.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 53.250 ------------------------------------------------------------------------------- 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 : 29.920 179.988 5816 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 % 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 *********************** 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 : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 176 average time/residue: 0.2664 time to fit residues: 66.1643 Evaluate side-chains 104 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.933 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0367 ------------------------------------------------------------------------------- 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: 8.9990 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: 0.9990 chunk 50 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 96 optimal weight: 5.9990 overall best weight: 1.8388 ------------------------------------------------------------------------------- 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** N 95 GLN ** 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: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8424 moved from start: 0.1775 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14032 Z= 0.213 Angle : 0.601 7.948 20419 Z= 0.362 Chirality : 0.033 0.130 2320 Planarity : 0.004 0.046 1398 Dihedral : 32.884 179.523 4292 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 0.63 % 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: 1.44 (0.30), residues: 752 helix: 1.35 (0.22), residues: 540 sheet: None (None), residues: 0 loop : 0.09 (0.40), residues: 212 *********************** 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 155 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 1.050 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 outliers start: 4 outliers final: 2 residues processed: 153 average time/residue: 0.2422 time to fit residues: 54.4211 Evaluate side-chains 101 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 99 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1425 time to fit residues: 1.4788 ------------------------------------------------------------------------------- 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: 9.9990 chunk 29 optimal weight: 5.9990 chunk 80 optimal weight: 6.9990 chunk 65 optimal weight: 5.9990 chunk 26 optimal weight: 0.0970 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: 3.9990 chunk 77 optimal weight: 6.9990 overall best weight: 4.4186 ------------------------------------------------------------------------------- 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** N 95 GLN ** O 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8534 moved from start: 0.3329 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= 0.353 Angle : 0.690 8.082 20419 Z= 0.407 Chirality : 0.038 0.165 2320 Planarity : 0.005 0.056 1398 Dihedral : 33.481 174.321 4292 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 23.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.16 % 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 (0.29), residues: 752 helix: 1.45 (0.22), residues: 538 sheet: None (None), residues: 0 loop : -0.08 (0.37), residues: 214 *********************** 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 135 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 134 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 134 average time/residue: 0.2527 time to fit residues: 49.2912 Evaluate side-chains 97 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 96 time to evaluate : 0.970 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1472 time to fit residues: 1.3229 ------------------------------------------------------------------------------- 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: 5.9990 chunk 72 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 46 optimal weight: 4.9990 chunk 64 optimal weight: 1.9990 chunk 96 optimal weight: 6.9990 chunk 102 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 chunk 27 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 55 GLN ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 93 GLN ** 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** Q 73 ASN ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.4029 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= 0.350 Angle : 0.675 7.888 20419 Z= 0.403 Chirality : 0.037 0.170 2320 Planarity : 0.005 0.038 1398 Dihedral : 33.670 176.716 4292 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 21.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.29 (0.30), residues: 752 helix: 1.32 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.23 (0.38), residues: 210 *********************** 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 128 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 126 time to evaluate : 1.015 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 127 average time/residue: 0.2574 time to fit residues: 47.9972 Evaluate side-chains 94 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.931 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1482 time to fit residues: 1.2671 ------------------------------------------------------------------------------- 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: 0.8980 chunk 1 optimal weight: 3.9990 chunk 76 optimal weight: 7.9990 chunk 42 optimal weight: 2.9990 chunk 87 optimal weight: 7.9990 chunk 70 optimal weight: 3.9990 chunk 0 optimal weight: 9.9990 chunk 52 optimal weight: 0.9990 chunk 91 optimal weight: 6.9990 chunk 25 optimal weight: 0.6980 chunk 34 optimal weight: 0.0050 overall best weight: 1.1198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 75 HIS M 104 GLN O 55 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.4070 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.040 14032 Z= 0.191 Angle : 0.600 8.302 20419 Z= 0.358 Chirality : 0.034 0.155 2320 Planarity : 0.004 0.041 1398 Dihedral : 33.348 179.133 4292 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 15.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer Outliers : 0.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.69 (0.30), residues: 752 helix: 1.64 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.14 (0.40), residues: 210 *********************** 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 153 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 150 time to evaluate : 0.926 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 outliers start: 3 outliers final: 3 residues processed: 151 average time/residue: 0.2348 time to fit residues: 52.2991 Evaluate side-chains 105 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 102 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1503 time to fit residues: 1.8225 ------------------------------------------------------------------------------- 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: 6.9990 chunk 20 optimal weight: 10.0000 chunk 60 optimal weight: 1.9990 chunk 25 optimal weight: 6.9990 chunk 102 optimal weight: 8.9990 chunk 85 optimal weight: 6.9990 chunk 47 optimal weight: 10.0000 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 chunk 53 optimal weight: 9.9990 chunk 98 optimal weight: 7.9990 overall best weight: 3.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** P 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.4533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 14032 Z= 0.301 Angle : 0.645 8.168 20419 Z= 0.383 Chirality : 0.036 0.157 2320 Planarity : 0.004 0.047 1398 Dihedral : 33.490 178.191 4292 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 20.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.16 % 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: 1.67 (0.30), residues: 752 helix: 1.66 (0.22), residues: 540 sheet: None (None), residues: 0 loop : -0.23 (0.39), residues: 212 *********************** 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 131 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 130 time to evaluate : 1.071 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 130 average time/residue: 0.2224 time to fit residues: 43.6588 Evaluate side-chains 94 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 0.994 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1408 ------------------------------------------------------------------------------- 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: 0.7980 chunk 74 optimal weight: 7.9990 chunk 86 optimal weight: 7.9990 chunk 57 optimal weight: 2.9990 chunk 102 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 62 optimal weight: 0.9980 chunk 47 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.4767 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 14032 Z= 0.237 Angle : 0.618 8.305 20419 Z= 0.369 Chirality : 0.035 0.148 2320 Planarity : 0.004 0.045 1398 Dihedral : 33.358 178.154 4292 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer Outliers : 0.16 % 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: 1.69 (0.30), residues: 752 helix: 1.67 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.22 (0.39), residues: 210 *********************** 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 140 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 139 time to evaluate : 1.009 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 140 average time/residue: 0.2481 time to fit residues: 51.2841 Evaluate side-chains 101 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.997 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1186 time to fit residues: 1.3267 ------------------------------------------------------------------------------- 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: 1.9990 chunk 20 optimal weight: 0.8980 chunk 19 optimal weight: 9.9990 chunk 64 optimal weight: 8.9990 chunk 69 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 9 optimal weight: 0.0570 chunk 80 optimal weight: 6.9990 chunk 92 optimal weight: 6.9990 chunk 97 optimal weight: 6.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.9904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.4976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 14032 Z= 0.220 Angle : 0.625 8.286 20419 Z= 0.371 Chirality : 0.035 0.168 2320 Planarity : 0.004 0.046 1398 Dihedral : 33.245 178.757 4292 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 18.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.30), residues: 752 helix: 1.62 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.24 (0.40), residues: 210 *********************** 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 144 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 144 time to evaluate : 0.952 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 144 average time/residue: 0.2662 time to fit residues: 56.0619 Evaluate side-chains 104 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 104 time to evaluate : 0.936 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1325 ------------------------------------------------------------------------------- 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: 5.9990 chunk 74 optimal weight: 7.9990 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 90 optimal weight: 10.0000 chunk 94 optimal weight: 7.9990 chunk 62 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 overall best weight: 6.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: M 112 GLN ** N 84 ASN ** 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: 0.8587 moved from start: 0.5829 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.009 0.058 14032 Z= 0.466 Angle : 0.774 8.594 20419 Z= 0.455 Chirality : 0.041 0.186 2320 Planarity : 0.005 0.037 1398 Dihedral : 33.962 176.358 4292 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 31.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.29), residues: 752 helix: 0.83 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.46 (0.39), residues: 208 *********************** 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 : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 128 average time/residue: 0.2468 time to fit residues: 46.3118 Evaluate side-chains 94 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 94 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0102 ------------------------------------------------------------------------------- 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: 1.9990 chunk 47 optimal weight: 9.9990 chunk 69 optimal weight: 0.7980 chunk 105 optimal weight: 10.0000 chunk 97 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 8 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 14032 Z= 0.206 Angle : 0.650 12.616 20419 Z= 0.383 Chirality : 0.036 0.169 2320 Planarity : 0.004 0.043 1398 Dihedral : 33.407 178.211 4292 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 17.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.28 (0.30), residues: 752 helix: 1.36 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.36 (0.40), residues: 210 ********************** 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 142 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.2492 time to fit residues: 52.0026 Evaluate side-chains 97 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 97 time to evaluate : 1.000 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1159 ------------------------------------------------------------------------------- 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: 4.9990 chunk 77 optimal weight: 7.9990 chunk 12 optimal weight: 8.9990 chunk 23 optimal weight: 10.0000 chunk 84 optimal weight: 6.9990 chunk 35 optimal weight: 1.9990 chunk 86 optimal weight: 7.9990 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 5.9990 chunk 73 optimal weight: 8.9990 chunk 4 optimal weight: 1.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.027653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2528 r_free = 0.2528 target = 0.020654 restraints weight = 180142.166| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2570 r_free = 0.2570 target = 0.021409 restraints weight = 87617.183| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.2597 r_free = 0.2597 target = 0.021926 restraints weight = 53723.251| |-----------------------------------------------------------------------------| r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.5799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 14032 Z= 0.281 Angle : 0.660 8.189 20419 Z= 0.391 Chirality : 0.036 0.182 2320 Planarity : 0.004 0.041 1398 Dihedral : 33.429 177.415 4292 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 22.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.30), residues: 752 helix: 1.47 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.34 (0.41), residues: 210 =============================================================================== Job complete usr+sys time: 1874.74 seconds wall clock time: 35 minutes 30.01 seconds (2130.01 seconds total)