Starting phenix.real_space_refine on Fri Feb 16 10:37:36 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf4_13367/02_2024/7pf4_13367.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf4_13367/02_2024/7pf4_13367.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf4_13367/02_2024/7pf4_13367.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf4_13367/02_2024/7pf4_13367.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf4_13367/02_2024/7pf4_13367.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf4_13367/02_2024/7pf4_13367.pdb" } resolution = 4.0 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= 0.003 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 334 5.49 5 S 10 5.16 5 C 7084 2.51 5 N 2431 2.21 5 O 3076 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 59": "OE1" <-> "OE2" Residue "K PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 52": "OE1" <-> "OE2" Residue "M TYR 57": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 93": "OE1" <-> "OE2" Residue "O PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "O TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "P GLU 52": "OE1" <-> "OE2" Residue "Q GLU 91": "OE1" <-> "OE2" Residue "Q GLU 92": "OE1" <-> "OE2" Residue "R PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 76": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12935 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: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Time building chain proxies: 7.03, per 1000 atoms: 0.54 Number of scatterers: 12935 At special positions: 0 Unit cell: (116.55, 152.25, 117.6, 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 334 15.00 O 3076 8.00 N 2431 7.00 C 7084 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: 7.54 Conformation dependent library (CDL) restraints added in 1.2 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: 34 helices and 8 sheets defined 71.1% alpha, 2.1% beta 165 base pairs and 285 stacking pairs defined. Time for finding SS restraints: 6.40 Creating SS restraints... Processing helix chain 'K' and resid 44 through 57 Processing helix chain 'K' and resid 63 through 79 removed outlier: 3.711A pdb=" N PHE K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N ASP K 77 " --> pdb=" O GLU K 73 " (cutoff:3.500A) removed outlier: 3.614A 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: 3.781A pdb=" N ILE K 124 " --> pdb=" O MET K 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 24 through 29 removed outlier: 3.992A pdb=" N GLN L 27 " --> pdb=" O ASP L 24 " (cutoff:3.500A) removed outlier: 3.549A 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 49 through 76 removed outlier: 4.207A pdb=" N GLU L 53 " --> pdb=" O LEU L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 82 through 94 Processing helix chain 'M' and resid 16 through 21 Processing helix chain 'M' and resid 26 through 36 removed outlier: 3.668A pdb=" N VAL M 30 " --> pdb=" O PRO M 26 " (cutoff:3.500A) Processing helix chain 'M' and resid 45 through 73 removed outlier: 4.053A 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 'N' and resid 37 through 49 removed outlier: 3.550A 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 Processing helix chain 'N' and resid 104 through 123 Processing helix chain 'O' and resid 44 through 57 Processing helix chain 'O' and resid 63 through 79 removed outlier: 3.764A pdb=" N PHE O 78 " --> pdb=" O ILE O 74 " (cutoff:3.500A) Processing helix chain 'O' and resid 85 through 114 Processing helix chain 'O' and resid 120 through 131 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: 3.759A pdb=" N GLU P 53 " --> pdb=" O LEU P 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASP P 68 " --> pdb=" O ASN P 64 " (cutoff:3.500A) Processing helix chain 'P' and resid 82 through 93 Processing helix chain 'Q' and resid 16 through 21 Processing helix chain 'Q' and resid 26 through 36 removed outlier: 3.669A pdb=" N VAL Q 30 " --> pdb=" O PRO Q 26 " (cutoff:3.500A) Processing helix chain 'Q' and resid 45 through 73 removed outlier: 4.285A 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 '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 103 through 123 removed outlier: 3.695A pdb=" N ALA R 107 " --> pdb=" O PRO R 103 " (cutoff:3.500A) removed outlier: 3.527A 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: 6.735A 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 'M' and resid 42 through 43 removed outlier: 7.229A pdb=" N ARG M 42 " --> pdb=" O ILE N 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'M' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'O' and resid 83 through 84 removed outlier: 6.675A pdb=" N ARG O 83 " --> pdb=" O VAL P 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'O' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'Q' and resid 42 through 43 removed outlier: 7.181A pdb=" N ARG Q 42 " --> pdb=" O ILE R 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'Q' and resid 77 through 78 399 hydrogen bonds defined for protein. 1188 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 846 hydrogen bond angles 0 basepair planarities 165 basepair parallelities 285 stacking parallelities Total time for adding SS restraints: 6.15 Time building geometry restraints manager: 7.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2644 1.34 - 1.46: 4652 1.46 - 1.58: 5866 1.58 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 13848 Sorted by residual: bond pdb=" C3' DG I 522 " pdb=" O3' DG I 522 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.35e+00 bond pdb=" C3' DG I 410 " pdb=" O3' DG I 410 " ideal model delta sigma weight residual 1.422 1.481 -0.059 3.00e-02 1.11e+03 3.85e+00 bond pdb=" C3' DG I 488 " pdb=" O3' DG I 488 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.57e+00 bond pdb=" C3' DT I 502 " pdb=" O3' DT I 502 " ideal model delta sigma weight residual 1.422 1.471 -0.049 3.00e-02 1.11e+03 2.62e+00 bond pdb=" CG GLU K 105 " pdb=" CD GLU K 105 " ideal model delta sigma weight residual 1.516 1.479 0.037 2.50e-02 1.60e+03 2.23e+00 ... (remaining 13843 not shown) Histogram of bond angle deviations from ideal: 95.19 - 102.69: 522 102.69 - 110.19: 5237 110.19 - 117.68: 6080 117.68 - 125.18: 7166 125.18 - 132.68: 1130 Bond angle restraints: 20135 Sorted by residual: angle pdb=" CA GLU K 97 " pdb=" CB GLU K 97 " pdb=" CG GLU K 97 " ideal model delta sigma weight residual 114.10 126.68 -12.58 2.00e+00 2.50e-01 3.95e+01 angle pdb=" C ILE M 87 " pdb=" N ARG M 88 " pdb=" CA ARG M 88 " ideal model delta sigma weight residual 122.73 112.87 9.86 1.61e+00 3.86e-01 3.75e+01 angle pdb=" N GLU K 97 " pdb=" CA GLU K 97 " pdb=" CB GLU K 97 " ideal model delta sigma weight residual 110.28 118.73 -8.45 1.55e+00 4.16e-01 2.97e+01 angle pdb=" N GLU K 105 " pdb=" CA GLU K 105 " pdb=" CB GLU K 105 " ideal model delta sigma weight residual 110.16 117.55 -7.39 1.48e+00 4.57e-01 2.49e+01 angle pdb=" CA LYS M 118 " pdb=" CB LYS M 118 " pdb=" CG LYS M 118 " ideal model delta sigma weight residual 114.10 122.32 -8.22 2.00e+00 2.50e-01 1.69e+01 ... (remaining 20130 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.22: 5688 35.22 - 70.44: 1736 70.44 - 105.66: 33 105.66 - 140.88: 2 140.88 - 176.09: 1 Dihedral angle restraints: 7460 sinusoidal: 5238 harmonic: 2222 Sorted by residual: dihedral pdb=" CA ARG L 23 " pdb=" C ARG L 23 " pdb=" N ASP L 24 " pdb=" CA ASP L 24 " ideal model delta harmonic sigma weight residual -180.00 -149.36 -30.64 0 5.00e+00 4.00e-02 3.76e+01 dihedral pdb=" CA ARG M 88 " pdb=" C ARG M 88 " pdb=" N ASN M 89 " pdb=" CA ASN M 89 " ideal model delta harmonic sigma weight residual 180.00 154.55 25.45 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" CA PRO M 26 " pdb=" C PRO M 26 " pdb=" N VAL M 27 " pdb=" CA VAL M 27 " ideal model delta harmonic sigma weight residual 180.00 155.83 24.17 0 5.00e+00 4.00e-02 2.34e+01 ... (remaining 7457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 1793 0.051 - 0.102: 403 0.102 - 0.153: 71 0.153 - 0.205: 14 0.205 - 0.256: 7 Chirality restraints: 2288 Sorted by residual: chirality pdb=" CA GLU K 97 " pdb=" N GLU K 97 " pdb=" C GLU K 97 " pdb=" CB GLU K 97 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.63e+00 chirality pdb=" CA PHE K 104 " pdb=" N PHE K 104 " pdb=" C PHE K 104 " pdb=" CB PHE K 104 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CG LEU N 45 " pdb=" CB LEU N 45 " pdb=" CD1 LEU N 45 " pdb=" CD2 LEU N 45 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.22e+00 ... (remaining 2285 not shown) Planarity restraints: 1390 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE M 25 " 0.065 5.00e-02 4.00e+02 9.96e-02 1.59e+01 pdb=" N PRO M 26 " -0.172 5.00e-02 4.00e+02 pdb=" CA PRO M 26 " 0.054 5.00e-02 4.00e+02 pdb=" CD PRO M 26 " 0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE M 79 " -0.053 5.00e-02 4.00e+02 7.93e-02 1.01e+01 pdb=" N PRO M 80 " 0.137 5.00e-02 4.00e+02 pdb=" CA PRO M 80 " -0.041 5.00e-02 4.00e+02 pdb=" CD PRO M 80 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS N 85 " 0.014 2.00e-02 2.50e+03 2.77e-02 7.68e+00 pdb=" C LYS N 85 " -0.048 2.00e-02 2.50e+03 pdb=" O LYS N 85 " 0.018 2.00e-02 2.50e+03 pdb=" N ARG N 86 " 0.016 2.00e-02 2.50e+03 ... (remaining 1387 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2610 2.79 - 3.31: 11699 3.31 - 3.84: 27751 3.84 - 4.37: 30869 4.37 - 4.90: 42548 Nonbonded interactions: 115477 Sorted by model distance: nonbonded pdb=" O THR M 76 " pdb=" OG1 THR N 52 " model vdw 2.258 2.440 nonbonded pdb=" NH2 ARG L 78 " pdb=" O THR L 80 " model vdw 2.325 2.520 nonbonded pdb=" N GLY Q 44 " pdb=" O ILE R 89 " model vdw 2.335 2.520 nonbonded pdb=" OH TYR Q 39 " pdb=" OE1 GLU R 71 " model vdw 2.336 2.440 nonbonded pdb=" N GLY M 44 " pdb=" O ILE N 89 " model vdw 2.336 2.520 ... (remaining 115472 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: 8.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.270 Check model and map are aligned: 0.230 Set scattering table: 0.140 Process input model: 44.290 Find NCS groups from input model: 0.470 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 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 : 0.005 0.063 13848 Z= 0.283 Angle : 0.887 12.577 20135 Z= 0.509 Chirality : 0.047 0.256 2288 Planarity : 0.007 0.100 1390 Dihedral : 29.722 176.094 6028 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 0.00 % Allowed : 0.63 % Favored : 99.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -0.80 (0.27), residues: 752 helix: -0.21 (0.20), residues: 534 sheet: None (None), residues: 0 loop : -1.02 (0.37), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS P 75 PHE 0.021 0.003 PHE N 65 TYR 0.038 0.003 TYR O 99 ARG 0.014 0.001 ARG P 45 *********************** 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 168 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 168 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 94 GLU cc_start: 0.8844 (mm-30) cc_final: 0.8532 (mm-30) REVERT: K 96 SER cc_start: 0.9070 (m) cc_final: 0.8859 (p) REVERT: K 99 TYR cc_start: 0.8860 (t80) cc_final: 0.8502 (t80) REVERT: K 106 ASP cc_start: 0.8751 (m-30) cc_final: 0.8529 (m-30) REVERT: L 49 LEU cc_start: 0.8980 (mp) cc_final: 0.8723 (mp) REVERT: M 25 PHE cc_start: 0.7803 (m-80) cc_final: 0.7563 (m-10) REVERT: N 52 THR cc_start: 0.8016 (t) cc_final: 0.7471 (t) REVERT: N 71 GLU cc_start: 0.8815 (tm-30) cc_final: 0.8271 (tt0) REVERT: N 95 GLN cc_start: 0.8630 (pp30) cc_final: 0.8075 (tm-30) REVERT: N 105 GLU cc_start: 0.7938 (tp30) cc_final: 0.7628 (tp30) REVERT: N 108 LYS cc_start: 0.9269 (ptmm) cc_final: 0.8530 (ptmm) REVERT: N 116 LYS cc_start: 0.9456 (tmmt) cc_final: 0.9185 (tmtt) REVERT: N 120 LYS cc_start: 0.7434 (mmtt) cc_final: 0.7008 (mttt) REVERT: O 97 GLU cc_start: 0.8496 (mt-10) cc_final: 0.8055 (mt-10) REVERT: Q 79 ILE cc_start: 0.8482 (mm) cc_final: 0.7912 (pt) REVERT: R 51 ASP cc_start: 0.8340 (p0) cc_final: 0.8091 (p0) REVERT: R 95 GLN cc_start: 0.8624 (tm130) cc_final: 0.8363 (tm-30) REVERT: R 102 LEU cc_start: 0.9333 (mt) cc_final: 0.9091 (mp) REVERT: R 105 GLU cc_start: 0.8324 (mp0) cc_final: 0.7885 (mp0) outliers start: 0 outliers final: 0 residues processed: 168 average time/residue: 0.2689 time to fit residues: 63.2892 Evaluate side-chains 119 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 6.9990 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 chunk 26 optimal weight: 8.9990 chunk 53 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 81 optimal weight: 8.9990 chunk 31 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 60 optimal weight: 4.9990 chunk 94 optimal weight: 7.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 82 HIS ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 55 GLN ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** R 47 GLN R 82 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13848 Z= 0.246 Angle : 0.664 10.711 20135 Z= 0.393 Chirality : 0.037 0.198 2288 Planarity : 0.005 0.067 1390 Dihedral : 32.462 172.931 4504 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 19.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.99 % Favored : 98.01 % Rotamer: Outliers : 1.57 % Allowed : 10.38 % Favored : 88.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.62 (0.29), residues: 752 helix: 0.89 (0.21), residues: 544 sheet: None (None), residues: 0 loop : -0.70 (0.39), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.010 0.002 HIS N 82 PHE 0.015 0.002 PHE P 61 TYR 0.015 0.002 TYR R 40 ARG 0.006 0.001 ARG L 23 *********************** 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 140 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 130 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 96 SER cc_start: 0.9162 (m) cc_final: 0.8896 (p) REVERT: K 104 PHE cc_start: 0.9271 (m-10) cc_final: 0.8755 (m-80) REVERT: K 105 GLU cc_start: 0.9156 (mp0) cc_final: 0.8901 (mp0) REVERT: L 59 LYS cc_start: 0.9337 (tppt) cc_final: 0.9117 (tppp) REVERT: M 89 ASN cc_start: 0.8878 (m-40) cc_final: 0.8641 (m-40) REVERT: N 85 LYS cc_start: 0.9345 (ttpt) cc_final: 0.9050 (ttpp) REVERT: N 105 GLU cc_start: 0.8039 (tp30) cc_final: 0.7586 (tp30) REVERT: N 108 LYS cc_start: 0.9323 (ptmm) cc_final: 0.8408 (ptmm) REVERT: N 116 LYS cc_start: 0.9492 (tmmt) cc_final: 0.9181 (tmtt) REVERT: N 120 LYS cc_start: 0.7713 (mmtt) cc_final: 0.7196 (mttt) REVERT: O 54 TYR cc_start: 0.8819 (m-80) cc_final: 0.8318 (m-80) REVERT: O 97 GLU cc_start: 0.8556 (mt-10) cc_final: 0.8194 (mt-10) REVERT: O 100 LEU cc_start: 0.9399 (mt) cc_final: 0.9128 (mt) REVERT: O 104 PHE cc_start: 0.9122 (m-10) cc_final: 0.8784 (m-10) REVERT: R 51 ASP cc_start: 0.8381 (p0) cc_final: 0.8143 (p0) REVERT: R 108 LYS cc_start: 0.9522 (mtmt) cc_final: 0.9293 (mtmm) outliers start: 10 outliers final: 8 residues processed: 135 average time/residue: 0.2457 time to fit residues: 47.7526 Evaluate side-chains 119 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 111 time to evaluate : 0.943 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 82 LEU Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 1.9990 chunk 29 optimal weight: 7.9990 chunk 78 optimal weight: 8.9990 chunk 64 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 94 optimal weight: 8.9990 chunk 102 optimal weight: 7.9990 chunk 84 optimal weight: 6.9990 chunk 93 optimal weight: 7.9990 chunk 32 optimal weight: 0.9980 chunk 75 optimal weight: 8.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: N 82 HIS ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** O 39 HIS ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 13848 Z= 0.336 Angle : 0.696 10.294 20135 Z= 0.408 Chirality : 0.037 0.162 2288 Planarity : 0.006 0.066 1390 Dihedral : 32.749 175.150 4504 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 24.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.20 % Allowed : 14.78 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.29), residues: 752 helix: 1.04 (0.21), residues: 548 sheet: None (None), residues: 0 loop : -0.80 (0.40), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.002 HIS P 75 PHE 0.020 0.002 PHE P 61 TYR 0.029 0.003 TYR P 88 ARG 0.004 0.001 ARG Q 29 *********************** 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 133 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 119 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: 0.8897 (m-80) cc_final: 0.8626 (m-80) REVERT: K 94 GLU cc_start: 0.8910 (mm-30) cc_final: 0.8560 (mm-30) REVERT: K 99 TYR cc_start: 0.9030 (t80) cc_final: 0.8763 (t80) REVERT: K 105 GLU cc_start: 0.9212 (mp0) cc_final: 0.8864 (mp0) REVERT: M 89 ASN cc_start: 0.8838 (m-40) cc_final: 0.8629 (m-40) REVERT: M 92 GLU cc_start: 0.8704 (pm20) cc_final: 0.8382 (pm20) REVERT: N 85 LYS cc_start: 0.9400 (ttpt) cc_final: 0.9087 (ttpp) REVERT: N 105 GLU cc_start: 0.8148 (tp30) cc_final: 0.7691 (tp30) REVERT: N 108 LYS cc_start: 0.9334 (ptmm) cc_final: 0.8586 (ptmm) REVERT: N 111 VAL cc_start: 0.9184 (t) cc_final: 0.8806 (p) REVERT: O 54 TYR cc_start: 0.8832 (m-80) cc_final: 0.8505 (m-80) REVERT: O 97 GLU cc_start: 0.8537 (mt-10) cc_final: 0.8119 (mt-10) REVERT: O 104 PHE cc_start: 0.9220 (m-10) cc_final: 0.8767 (m-10) REVERT: R 108 LYS cc_start: 0.9545 (mtmt) cc_final: 0.9308 (mtmm) outliers start: 14 outliers final: 12 residues processed: 125 average time/residue: 0.2543 time to fit residues: 46.0930 Evaluate side-chains 123 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 119 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 7.9990 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 45 optimal weight: 8.9990 chunk 63 optimal weight: 0.0670 chunk 94 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 89 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 83 optimal weight: 4.9990 overall best weight: 2.4124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 104 GLN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.3925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 13848 Z= 0.258 Angle : 0.650 10.962 20135 Z= 0.384 Chirality : 0.035 0.152 2288 Planarity : 0.005 0.064 1390 Dihedral : 32.605 173.926 4504 Min Nonbonded Distance : 2.155 Molprobity Statistics. All-atom Clashscore : 21.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 2.52 % Allowed : 16.04 % Favored : 81.45 % 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: 1.11 (0.30), residues: 752 helix: 1.29 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.68 (0.41), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.008 0.001 HIS N 49 PHE 0.018 0.002 PHE P 61 TYR 0.019 0.002 TYR N 40 ARG 0.004 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 144 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 128 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 revert: symmetry clash revert: symmetry clash REVERT: K 54 TYR cc_start: 0.8847 (m-80) cc_final: 0.8510 (m-80) REVERT: K 94 GLU cc_start: 0.8917 (mm-30) cc_final: 0.8609 (mm-30) REVERT: K 104 PHE cc_start: 0.9392 (m-10) cc_final: 0.9066 (m-10) REVERT: L 53 GLU cc_start: 0.8678 (pt0) cc_final: 0.8214 (pm20) REVERT: N 85 LYS cc_start: 0.9390 (ttpt) cc_final: 0.9053 (ttpp) REVERT: N 105 GLU cc_start: 0.8156 (tp30) cc_final: 0.7698 (tp30) REVERT: N 108 LYS cc_start: 0.9293 (ptmm) cc_final: 0.8436 (ptmm) REVERT: N 111 VAL cc_start: 0.9270 (t) cc_final: 0.9021 (p) REVERT: O 54 TYR cc_start: 0.8889 (m-80) cc_final: 0.8628 (m-80) REVERT: O 97 GLU cc_start: 0.8477 (mt-10) cc_final: 0.7999 (mt-10) REVERT: O 104 PHE cc_start: 0.9189 (m-10) cc_final: 0.8878 (m-10) REVERT: P 88 TYR cc_start: 0.7719 (m-80) cc_final: 0.7516 (m-80) REVERT: Q 84 GLN cc_start: 0.5666 (tm-30) cc_final: 0.5364 (tm-30) REVERT: R 108 LYS cc_start: 0.9520 (mtmt) cc_final: 0.9278 (mtmm) outliers start: 16 outliers final: 10 residues processed: 136 average time/residue: 0.2433 time to fit residues: 48.5985 Evaluate side-chains 125 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 115 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 80 THR Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 71 THR Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.8980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 8.9990 chunk 41 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 3.9990 chunk 0 optimal weight: 20.0000 chunk 51 optimal weight: 0.9980 chunk 90 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7791 moved from start: 0.4123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13848 Z= 0.199 Angle : 0.627 11.894 20135 Z= 0.367 Chirality : 0.034 0.156 2288 Planarity : 0.005 0.061 1390 Dihedral : 32.381 172.042 4504 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 17.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.20 % Allowed : 18.08 % Favored : 79.72 % 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: 1.33 (0.30), residues: 752 helix: 1.48 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.62 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 75 PHE 0.016 0.002 PHE O 67 TYR 0.018 0.002 TYR R 40 ARG 0.004 0.000 ARG M 20 *********************** 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 145 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 131 time to evaluate : 0.918 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: 0.8769 (m-80) cc_final: 0.8394 (m-80) REVERT: K 85 GLN cc_start: 0.7306 (OUTLIER) cc_final: 0.6977 (pm20) REVERT: K 94 GLU cc_start: 0.8848 (mm-30) cc_final: 0.8551 (mm-30) REVERT: K 104 PHE cc_start: 0.9405 (m-10) cc_final: 0.9197 (m-10) REVERT: L 53 GLU cc_start: 0.8578 (pt0) cc_final: 0.8190 (pm20) REVERT: N 85 LYS cc_start: 0.9339 (ttpt) cc_final: 0.9021 (ttpp) REVERT: N 95 GLN cc_start: 0.8700 (pp30) cc_final: 0.8266 (pp30) REVERT: N 108 LYS cc_start: 0.9292 (ptmm) cc_final: 0.8778 (pttp) REVERT: O 54 TYR cc_start: 0.8843 (m-80) cc_final: 0.8570 (m-80) REVERT: O 55 GLN cc_start: 0.8640 (tp40) cc_final: 0.8176 (mm-40) REVERT: O 97 GLU cc_start: 0.8445 (mt-10) cc_final: 0.8063 (mt-10) REVERT: O 104 PHE cc_start: 0.9194 (m-10) cc_final: 0.8754 (m-10) REVERT: O 120 MET cc_start: 0.4100 (mtt) cc_final: 0.3798 (mtt) REVERT: P 88 TYR cc_start: 0.7229 (m-80) cc_final: 0.6953 (m-10) REVERT: R 85 LYS cc_start: 0.9455 (mmtt) cc_final: 0.9253 (mmtt) REVERT: R 105 GLU cc_start: 0.8096 (mp0) cc_final: 0.7849 (mp0) REVERT: R 108 LYS cc_start: 0.9508 (mtmt) cc_final: 0.9252 (mtmm) outliers start: 14 outliers final: 8 residues processed: 139 average time/residue: 0.2640 time to fit residues: 53.8541 Evaluate side-chains 131 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 16 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 8.9990 chunk 19 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 100 optimal weight: 6.9990 chunk 83 optimal weight: 6.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.9990 chunk 33 optimal weight: 0.9990 chunk 52 optimal weight: 0.0970 chunk 97 optimal weight: 8.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** M 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** Q 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.4329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 13848 Z= 0.203 Angle : 0.623 10.898 20135 Z= 0.365 Chirality : 0.034 0.216 2288 Planarity : 0.004 0.059 1390 Dihedral : 32.332 171.146 4504 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 18.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.89 % Allowed : 19.65 % Favored : 78.46 % 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: 1.59 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.57 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 75 PHE 0.019 0.002 PHE P 61 TYR 0.014 0.002 TYR P 88 ARG 0.002 0.000 ARG Q 17 *********************** 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 136 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.016 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: K 54 TYR cc_start: 0.8790 (m-80) cc_final: 0.8449 (m-80) REVERT: K 85 GLN cc_start: 0.7181 (OUTLIER) cc_final: 0.6843 (pm20) REVERT: K 94 GLU cc_start: 0.8819 (mm-30) cc_final: 0.8509 (mm-30) REVERT: K 104 PHE cc_start: 0.9381 (m-10) cc_final: 0.9178 (m-10) REVERT: L 53 GLU cc_start: 0.8588 (pt0) cc_final: 0.8255 (pm20) REVERT: M 89 ASN cc_start: 0.8654 (m-40) cc_final: 0.8449 (m-40) REVERT: N 85 LYS cc_start: 0.9342 (ttpt) cc_final: 0.9031 (ttpp) REVERT: N 95 GLN cc_start: 0.8718 (pp30) cc_final: 0.8230 (pp30) REVERT: N 108 LYS cc_start: 0.9247 (ptmm) cc_final: 0.8701 (pttp) REVERT: O 54 TYR cc_start: 0.8802 (m-80) cc_final: 0.8543 (m-80) REVERT: O 55 GLN cc_start: 0.8656 (tp40) cc_final: 0.8076 (mm-40) REVERT: O 97 GLU cc_start: 0.8407 (mt-10) cc_final: 0.8007 (mt-10) REVERT: O 104 PHE cc_start: 0.9138 (m-10) cc_final: 0.8677 (m-10) REVERT: Q 15 LYS cc_start: 0.9174 (tppt) cc_final: 0.8952 (tptp) REVERT: R 108 LYS cc_start: 0.9498 (mtmt) cc_final: 0.9224 (mtmm) outliers start: 12 outliers final: 10 residues processed: 133 average time/residue: 0.2397 time to fit residues: 47.0425 Evaluate side-chains 130 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 119 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain O residue 87 SER Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.8980 chunk 57 optimal weight: 0.6980 chunk 73 optimal weight: 10.0000 chunk 56 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 100 optimal weight: 6.9990 chunk 62 optimal weight: 6.9990 chunk 61 optimal weight: 0.9980 chunk 46 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 84 GLN ** N 84 ASN ** 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: 0.7750 moved from start: 0.4591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 13848 Z= 0.187 Angle : 0.622 11.161 20135 Z= 0.363 Chirality : 0.034 0.215 2288 Planarity : 0.004 0.059 1390 Dihedral : 32.189 170.169 4504 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 17.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.52 % Allowed : 19.50 % Favored : 77.99 % 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: 1.40 (0.30), residues: 752 helix: 1.50 (0.22), residues: 542 sheet: None (None), residues: 0 loop : -0.50 (0.41), residues: 210 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 75 PHE 0.033 0.002 PHE P 61 TYR 0.015 0.001 TYR L 72 ARG 0.002 0.000 ARG Q 42 *********************** 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 141 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 125 time to evaluate : 0.974 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: K 54 TYR cc_start: 0.8751 (m-80) cc_final: 0.8352 (m-80) REVERT: K 85 GLN cc_start: 0.7267 (OUTLIER) cc_final: 0.6947 (pm20) REVERT: K 94 GLU cc_start: 0.8786 (mm-30) cc_final: 0.8514 (mm-30) REVERT: K 104 PHE cc_start: 0.9378 (m-10) cc_final: 0.9170 (m-10) REVERT: K 105 GLU cc_start: 0.9192 (mt-10) cc_final: 0.8660 (mp0) REVERT: L 53 GLU cc_start: 0.8442 (pt0) cc_final: 0.8179 (pm20) REVERT: M 89 ASN cc_start: 0.8604 (m-40) cc_final: 0.8371 (m-40) REVERT: N 85 LYS cc_start: 0.9325 (ttpt) cc_final: 0.8912 (ttpp) REVERT: N 95 GLN cc_start: 0.8722 (pp30) cc_final: 0.7978 (pp30) REVERT: N 108 LYS cc_start: 0.9251 (ptmm) cc_final: 0.8764 (pttp) REVERT: N 120 LYS cc_start: 0.8827 (mmtp) cc_final: 0.8570 (mmtt) REVERT: O 54 TYR cc_start: 0.8760 (m-80) cc_final: 0.8508 (m-80) REVERT: O 55 GLN cc_start: 0.8612 (tp40) cc_final: 0.8123 (mm-40) REVERT: O 97 GLU cc_start: 0.8400 (mt-10) cc_final: 0.7980 (mt-10) REVERT: O 104 PHE cc_start: 0.9112 (m-10) cc_final: 0.8658 (m-10) REVERT: R 71 GLU cc_start: 0.8939 (tp30) cc_final: 0.8707 (tp30) REVERT: R 108 LYS cc_start: 0.9503 (mtmt) cc_final: 0.9211 (mtmm) outliers start: 16 outliers final: 11 residues processed: 135 average time/residue: 0.2551 time to fit residues: 50.2350 Evaluate side-chains 131 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 119 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 80 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 chunk 68 optimal weight: 0.5980 chunk 49 optimal weight: 2.9990 chunk 9 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 96 optimal weight: 6.9990 chunk 87 optimal weight: 7.9990 chunk 93 optimal weight: 7.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.5059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13848 Z= 0.270 Angle : 0.665 12.549 20135 Z= 0.383 Chirality : 0.036 0.260 2288 Planarity : 0.005 0.060 1390 Dihedral : 32.423 171.003 4504 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 22.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 2.52 % Allowed : 19.65 % Favored : 77.83 % 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: 1.22 (0.30), residues: 752 helix: 1.33 (0.22), residues: 552 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 75 PHE 0.032 0.003 PHE P 61 TYR 0.016 0.002 TYR M 57 ARG 0.003 0.000 ARG M 81 *********************** 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 136 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 120 time to evaluate : 0.994 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: 0.8890 (m-80) cc_final: 0.8476 (m-80) REVERT: K 85 GLN cc_start: 0.7185 (OUTLIER) cc_final: 0.6878 (pm20) REVERT: K 94 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8593 (mm-30) REVERT: K 105 GLU cc_start: 0.9222 (mt-10) cc_final: 0.8689 (mp0) REVERT: L 53 GLU cc_start: 0.8508 (pt0) cc_final: 0.8259 (pm20) REVERT: N 85 LYS cc_start: 0.9354 (ttpt) cc_final: 0.9049 (ttpp) REVERT: N 95 GLN cc_start: 0.8862 (pp30) cc_final: 0.8063 (pp30) REVERT: N 99 ARG cc_start: 0.9065 (mtt90) cc_final: 0.8795 (mtt90) REVERT: N 108 LYS cc_start: 0.9193 (ptmm) cc_final: 0.8700 (pttp) REVERT: O 54 TYR cc_start: 0.8862 (m-80) cc_final: 0.8611 (m-80) REVERT: O 97 GLU cc_start: 0.8469 (mt-10) cc_final: 0.8076 (mt-10) REVERT: O 104 PHE cc_start: 0.9193 (m-10) cc_final: 0.8721 (m-10) REVERT: O 120 MET cc_start: 0.5204 (mtt) cc_final: 0.4951 (mtt) REVERT: R 108 LYS cc_start: 0.9526 (mtmt) cc_final: 0.9262 (mtmm) outliers start: 16 outliers final: 15 residues processed: 131 average time/residue: 0.2470 time to fit residues: 47.0553 Evaluate side-chains 131 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 115 time to evaluate : 0.973 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 46 ILE Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 87 ILE Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 48 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 7.9990 chunk 56 optimal weight: 0.8980 chunk 40 optimal weight: 4.9990 chunk 73 optimal weight: 10.0000 chunk 28 optimal weight: 0.9980 chunk 84 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 61 optimal weight: 2.9990 chunk 98 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** O 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.5630 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13848 Z= 0.268 Angle : 0.685 12.190 20135 Z= 0.392 Chirality : 0.037 0.286 2288 Planarity : 0.005 0.059 1390 Dihedral : 32.506 171.056 4504 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 22.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.19 % Favored : 96.81 % Rotamer: Outliers : 2.99 % Allowed : 21.07 % Favored : 75.94 % 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: 0.91 (0.30), residues: 752 helix: 1.06 (0.22), residues: 554 sheet: None (None), residues: 0 loop : -0.52 (0.42), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS P 75 PHE 0.038 0.003 PHE P 61 TYR 0.025 0.002 TYR M 57 ARG 0.008 0.000 ARG P 92 *********************** 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 144 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 125 time to evaluate : 1.070 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: K 85 GLN cc_start: 0.7336 (OUTLIER) cc_final: 0.6951 (pm20) REVERT: K 94 GLU cc_start: 0.8769 (mm-30) cc_final: 0.8565 (mm-30) REVERT: K 105 GLU cc_start: 0.9100 (mt-10) cc_final: 0.8562 (mp0) REVERT: L 86 VAL cc_start: 0.7514 (t) cc_final: 0.7306 (t) REVERT: N 85 LYS cc_start: 0.9350 (ttpt) cc_final: 0.9084 (ttpp) REVERT: N 89 ILE cc_start: 0.7777 (OUTLIER) cc_final: 0.7201 (tp) REVERT: N 95 GLN cc_start: 0.8887 (pp30) cc_final: 0.8069 (pp30) REVERT: N 108 LYS cc_start: 0.9155 (ptmm) cc_final: 0.8636 (pttp) REVERT: N 120 LYS cc_start: 0.9186 (mmtt) cc_final: 0.8615 (mmtt) REVERT: O 54 TYR cc_start: 0.9008 (m-80) cc_final: 0.8652 (m-80) REVERT: O 97 GLU cc_start: 0.8429 (mt-10) cc_final: 0.8048 (mt-10) REVERT: O 104 PHE cc_start: 0.9197 (m-10) cc_final: 0.8706 (m-10) REVERT: Q 84 GLN cc_start: 0.5681 (tm-30) cc_final: 0.5398 (tm-30) REVERT: R 108 LYS cc_start: 0.9531 (mtmt) cc_final: 0.9288 (mtmm) outliers start: 19 outliers final: 15 residues processed: 137 average time/residue: 0.2737 time to fit residues: 53.7038 Evaluate side-chains 133 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 116 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 96 SER Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 103 LEU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain N residue 122 THR Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain P residue 86 VAL Chi-restraints excluded: chain Q residue 16 THR Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 5.9990 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 7.9990 chunk 95 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 8 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 50 optimal weight: 0.8980 chunk 65 optimal weight: 0.0980 chunk 87 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** M 38 ASN ** N 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.5725 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13848 Z= 0.213 Angle : 0.671 13.050 20135 Z= 0.382 Chirality : 0.036 0.306 2288 Planarity : 0.004 0.058 1390 Dihedral : 32.365 169.871 4504 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 19.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 2.04 % Allowed : 23.11 % Favored : 74.84 % 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: 1.06 (0.30), residues: 752 helix: 1.25 (0.22), residues: 548 sheet: None (None), residues: 0 loop : -0.67 (0.42), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS P 75 PHE 0.048 0.003 PHE P 61 TYR 0.016 0.002 TYR K 99 ARG 0.003 0.000 ARG P 92 ********************** 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 136 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 1.081 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 85 GLN cc_start: 0.7246 (OUTLIER) cc_final: 0.6911 (pm20) REVERT: K 94 GLU cc_start: 0.8744 (mm-30) cc_final: 0.8482 (mm-30) REVERT: K 120 MET cc_start: 0.6382 (mtt) cc_final: 0.6124 (mtt) REVERT: L 74 GLU cc_start: 0.9305 (mm-30) cc_final: 0.9032 (mm-30) REVERT: M 36 LYS cc_start: 0.8582 (mtpp) cc_final: 0.8018 (mppt) REVERT: N 85 LYS cc_start: 0.9311 (ttpt) cc_final: 0.9028 (ttpp) REVERT: N 89 ILE cc_start: 0.7694 (OUTLIER) cc_final: 0.7193 (tp) REVERT: N 95 GLN cc_start: 0.8877 (pp30) cc_final: 0.8197 (pp30) REVERT: N 108 LYS cc_start: 0.9138 (ptmm) cc_final: 0.8603 (pttp) REVERT: N 120 LYS cc_start: 0.9280 (mmtt) cc_final: 0.8951 (mmtm) REVERT: O 104 PHE cc_start: 0.9125 (m-10) cc_final: 0.8667 (m-10) REVERT: Q 84 GLN cc_start: 0.5782 (tm-30) cc_final: 0.5499 (tm-30) REVERT: R 108 LYS cc_start: 0.9513 (mtmt) cc_final: 0.9261 (mtmm) outliers start: 13 outliers final: 10 residues processed: 131 average time/residue: 0.2637 time to fit residues: 49.5162 Evaluate side-chains 132 residues out of total 636 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 74 ILE Chi-restraints excluded: chain K residue 85 GLN Chi-restraints excluded: chain K residue 97 GLU Chi-restraints excluded: chain K residue 125 GLN Chi-restraints excluded: chain L residue 66 ILE Chi-restraints excluded: chain L residue 71 THR Chi-restraints excluded: chain M residue 114 VAL Chi-restraints excluded: chain N residue 89 ILE Chi-restraints excluded: chain P residue 21 VAL Chi-restraints excluded: chain R residue 42 TYR Chi-restraints excluded: chain R residue 48 VAL Chi-restraints excluded: chain R residue 80 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 6.9990 chunk 12 optimal weight: 4.9990 chunk 22 optimal weight: 0.9990 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 0.9980 chunk 84 optimal weight: 7.9990 chunk 10 optimal weight: 3.9990 chunk 15 optimal weight: 5.9990 chunk 72 optimal weight: 10.0000 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 85 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 = 0.3712 r_free = 0.3712 target = 0.054879 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.043171 restraints weight = 109825.626| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.044240 restraints weight = 63176.436| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3362 r_free = 0.3362 target = 0.044912 restraints weight = 43655.726| |-----------------------------------------------------------------------------| r_work (final): 0.3326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 13848 Z= 0.252 Angle : 0.682 12.426 20135 Z= 0.388 Chirality : 0.036 0.297 2288 Planarity : 0.005 0.057 1390 Dihedral : 32.417 169.962 4504 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 22.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.99 % Favored : 96.01 % Rotamer: Outliers : 2.20 % Allowed : 24.06 % Favored : 73.74 % 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: 0.98 (0.30), residues: 752 helix: 1.16 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.62 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS P 75 PHE 0.031 0.003 PHE K 104 TYR 0.027 0.002 TYR M 57 ARG 0.004 0.000 ARG K 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2027.20 seconds wall clock time: 38 minutes 28.05 seconds (2308.05 seconds total)