Starting phenix.real_space_refine on Fri Mar 15 17:49:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/03_2024/7y00_33536.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/03_2024/7y00_33536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/03_2024/7y00_33536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/03_2024/7y00_33536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/03_2024/7y00_33536.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/03_2024/7y00_33536.pdb" } resolution = 3.96 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 310 5.49 5 S 14 5.16 5 C 6823 2.51 5 N 2339 2.21 5 O 2925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A GLU 97": "OE1" <-> "OE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D ASP 48": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 32": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12411 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3166 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Chain: "J" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3189 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Time building chain proxies: 5.41, per 1000 atoms: 0.44 Number of scatterers: 12411 At special positions: 0 Unit cell: (116.6, 147.34, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 310 15.00 O 2925 8.00 N 2339 7.00 C 6823 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: 5.43 Conformation dependent library (CDL) restraints added in 870.4 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.5% alpha, 3.1% beta 153 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 4.78 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.096A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.292A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.117A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.995A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.537A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.553A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.268A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.523A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.757A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.501A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.761A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.342A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.547A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 415 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 395 hydrogen bonds 786 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 3.48 Time building geometry restraints manager: 5.82 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: 2627 1.34 - 1.46: 4279 1.46 - 1.57: 5716 1.57 - 1.69: 618 1.69 - 1.81: 24 Bond restraints: 13264 Sorted by residual: bond pdb=" C1' DG J 31 " pdb=" N9 DG J 31 " ideal model delta sigma weight residual 1.460 1.391 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ILE C 87 " pdb=" CA ILE C 87 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.19e-02 7.06e+03 7.08e+00 bond pdb=" N ILE H 66 " pdb=" CA ILE H 66 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 7.02e+00 bond pdb=" N ILE G 87 " pdb=" CA ILE G 87 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N ILE D 66 " pdb=" CA ILE D 66 " ideal model delta sigma weight residual 1.461 1.491 -0.029 1.17e-02 7.31e+03 6.31e+00 ... (remaining 13259 not shown) Histogram of bond angle deviations from ideal: 98.49 - 105.29: 1342 105.29 - 112.09: 7243 112.09 - 118.90: 3393 118.90 - 125.70: 6225 125.70 - 132.50: 1035 Bond angle restraints: 19238 Sorted by residual: angle pdb=" N GLN E 76 " pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " ideal model delta sigma weight residual 110.32 117.12 -6.80 1.70e+00 3.46e-01 1.60e+01 angle pdb=" C ALA E 75 " pdb=" N GLN E 76 " pdb=" CA GLN E 76 " ideal model delta sigma weight residual 120.60 115.14 5.46 1.60e+00 3.91e-01 1.16e+01 angle pdb=" N ILE D 66 " pdb=" CA ILE D 66 " pdb=" C ILE D 66 " ideal model delta sigma weight residual 110.42 107.17 3.25 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N ILE H 66 " pdb=" CA ILE H 66 " pdb=" C ILE H 66 " ideal model delta sigma weight residual 110.42 107.39 3.03 9.60e-01 1.09e+00 9.97e+00 angle pdb=" C GLU G 56 " pdb=" CA GLU G 56 " pdb=" CB GLU G 56 " ideal model delta sigma weight residual 110.88 105.92 4.96 1.57e+00 4.06e-01 9.96e+00 ... (remaining 19233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4655 17.78 - 35.56: 1125 35.56 - 53.34: 1042 53.34 - 71.13: 324 71.13 - 88.91: 19 Dihedral angle restraints: 7165 sinusoidal: 4961 harmonic: 2204 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " pdb=" CG1 ILE G 87 " pdb=" CD1 ILE G 87 " ideal model delta sinusoidal sigma weight residual 180.00 122.74 57.26 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -138.72 -41.28 2 1.50e+01 4.44e-03 9.29e+00 ... (remaining 7162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1839 0.046 - 0.091: 267 0.091 - 0.137: 65 0.137 - 0.182: 8 0.182 - 0.228: 5 Chirality restraints: 2184 Sorted by residual: chirality pdb=" CA GLU C 61 " pdb=" N GLU C 61 " pdb=" C GLU C 61 " pdb=" CB GLU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 2181 not shown) Planarity restraints: 1361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 52 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C ALA G 52 " 0.077 2.00e-02 2.50e+03 pdb=" O ALA G 52 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA G 53 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C LYS F 59 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 87 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C SER E 87 " -0.028 2.00e-02 2.50e+03 pdb=" O SER E 87 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA E 88 " 0.010 2.00e-02 2.50e+03 ... (remaining 1358 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 27 2.35 - 2.99: 5762 2.99 - 3.63: 21890 3.63 - 4.26: 33094 4.26 - 4.90: 47127 Nonbonded interactions: 107900 Sorted by model distance: nonbonded pdb=" CD1 LEU G 23 " pdb=" OE1 GLU G 56 " model vdw 1.717 3.460 nonbonded pdb=" N GLN G 24 " pdb=" OE2 GLU G 56 " model vdw 2.100 2.520 nonbonded pdb=" O2 DC I 49 " pdb=" N2 DG J 121 " model vdw 2.194 2.496 nonbonded pdb=" OG1 THR G 16 " pdb=" OP1 DA J 55 " model vdw 2.195 2.440 nonbonded pdb=" OG SER D 84 " pdb=" OP1 DG I 38 " model vdw 2.223 2.440 ... (remaining 107895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=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: 1.020 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.830 Check model and map are aligned: 0.160 Set scattering table: 0.100 Process input model: 32.950 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.170 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13264 Z= 0.213 Angle : 0.687 8.646 19238 Z= 0.435 Chirality : 0.038 0.228 2184 Planarity : 0.005 0.045 1361 Dihedral : 27.461 88.908 5745 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.31 % Allowed : 1.10 % Favored : 98.58 % 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: 0.85 (0.28), residues: 746 helix: 1.00 (0.20), residues: 549 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.015 0.002 PHE G 25 TYR 0.026 0.002 TYR B 88 ARG 0.005 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 1.025 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 49 LEU cc_start: 0.9175 (mt) cc_final: 0.8923 (mt) REVERT: B 53 GLU cc_start: 0.8655 (mp0) cc_final: 0.8427 (mp0) REVERT: C 90 ASP cc_start: 0.8518 (t0) cc_final: 0.8211 (t70) REVERT: D 42 LEU cc_start: 0.9576 (tp) cc_final: 0.9318 (tp) REVERT: D 65 ASP cc_start: 0.8916 (t0) cc_final: 0.8542 (t0) REVERT: E 62 ILE cc_start: 0.9611 (tt) cc_final: 0.9371 (tt) REVERT: E 74 ILE cc_start: 0.9547 (tt) cc_final: 0.9331 (tt) REVERT: F 63 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8918 (mp0) REVERT: G 64 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8473 (tm-30) REVERT: H 45 VAL cc_start: 0.9003 (t) cc_final: 0.8748 (t) REVERT: H 65 ASP cc_start: 0.9048 (t70) cc_final: 0.8844 (t0) REVERT: H 73 GLU cc_start: 0.9031 (tp30) cc_final: 0.8540 (tp30) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.2390 time to fit residues: 65.3590 Evaluate side-chains 136 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 9.9990 chunk 52 optimal weight: 0.6980 chunk 41 optimal weight: 0.9990 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.0980 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 5.9990 chunk 92 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8304 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13264 Z= 0.223 Angle : 0.609 7.357 19238 Z= 0.357 Chirality : 0.035 0.193 2184 Planarity : 0.005 0.056 1361 Dihedral : 31.279 89.439 4224 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 10.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 1.42 % Allowed : 14.65 % Favored : 83.94 % 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: 2.25 (0.30), residues: 746 helix: 2.13 (0.21), residues: 549 sheet: None (None), residues: 0 loop : -0.34 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 113 PHE 0.015 0.002 PHE E 67 TYR 0.022 0.002 TYR C 50 ARG 0.006 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 165 time to evaluate : 1.044 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: A 73 GLU cc_start: 0.8953 (tt0) cc_final: 0.8212 (tt0) REVERT: A 105 GLU cc_start: 0.8923 (tm-30) cc_final: 0.8528 (tm-30) REVERT: B 49 LEU cc_start: 0.9363 (mt) cc_final: 0.8601 (mt) REVERT: B 53 GLU cc_start: 0.8881 (mp0) cc_final: 0.8569 (mp0) REVERT: B 63 GLU cc_start: 0.8967 (OUTLIER) cc_final: 0.8601 (mp0) REVERT: B 74 GLU cc_start: 0.8529 (mt-10) cc_final: 0.8264 (mt-10) REVERT: B 88 TYR cc_start: 0.8841 (m-10) cc_final: 0.8595 (m-10) REVERT: C 36 LYS cc_start: 0.9540 (ttmt) cc_final: 0.9323 (ttmm) REVERT: C 90 ASP cc_start: 0.8783 (t0) cc_final: 0.8560 (t70) REVERT: D 65 ASP cc_start: 0.8883 (t0) cc_final: 0.8574 (t0) REVERT: D 68 GLU cc_start: 0.8804 (tm-30) cc_final: 0.8447 (tm-30) REVERT: F 88 TYR cc_start: 0.8580 (m-80) cc_final: 0.8207 (m-80) REVERT: F 93 GLN cc_start: 0.9314 (tp40) cc_final: 0.9085 (tp40) REVERT: H 73 GLU cc_start: 0.9150 (tp30) cc_final: 0.8750 (tp30) REVERT: H 80 TYR cc_start: 0.7720 (m-10) cc_final: 0.6460 (m-10) outliers start: 9 outliers final: 4 residues processed: 171 average time/residue: 0.2238 time to fit residues: 56.0963 Evaluate side-chains 138 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 133 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 92 optimal weight: 8.9990 chunk 100 optimal weight: 6.9990 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 0.8980 chunk 74 optimal weight: 7.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN B 93 GLN C 24 GLN D 44 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8556 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 13264 Z= 0.257 Angle : 0.622 10.603 19238 Z= 0.361 Chirality : 0.036 0.246 2184 Planarity : 0.005 0.052 1361 Dihedral : 31.715 89.518 4224 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 3.78 % Allowed : 15.91 % Favored : 80.31 % 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: 2.41 (0.31), residues: 746 helix: 2.27 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.34 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.028 0.002 PHE E 67 TYR 0.022 0.002 TYR C 39 ARG 0.004 0.001 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 146 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8609 (tm-30) REVERT: B 53 GLU cc_start: 0.9105 (mp0) cc_final: 0.8561 (mp0) REVERT: B 63 GLU cc_start: 0.8872 (OUTLIER) cc_final: 0.8552 (mp0) REVERT: B 74 GLU cc_start: 0.8409 (mt-10) cc_final: 0.8180 (mt-10) REVERT: B 84 MET cc_start: 0.9342 (mmm) cc_final: 0.8989 (mmm) REVERT: B 88 TYR cc_start: 0.9018 (m-10) cc_final: 0.8395 (m-10) REVERT: C 36 LYS cc_start: 0.9648 (ttmt) cc_final: 0.9431 (ttmm) REVERT: C 56 GLU cc_start: 0.8625 (tt0) cc_final: 0.8397 (tp30) REVERT: C 61 GLU cc_start: 0.8831 (OUTLIER) cc_final: 0.8419 (mm-30) REVERT: D 68 GLU cc_start: 0.8867 (tm-30) cc_final: 0.8600 (tm-30) REVERT: E 120 MET cc_start: 0.7802 (mpp) cc_final: 0.7392 (mpp) REVERT: F 53 GLU cc_start: 0.9218 (mp0) cc_final: 0.8993 (mp0) REVERT: H 73 GLU cc_start: 0.9262 (tp30) cc_final: 0.8883 (tp30) outliers start: 24 outliers final: 10 residues processed: 157 average time/residue: 0.2313 time to fit residues: 52.8585 Evaluate side-chains 133 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 86 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 0.0070 chunk 93 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 overall best weight: 0.9200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13264 Z= 0.186 Angle : 0.585 8.522 19238 Z= 0.341 Chirality : 0.033 0.139 2184 Planarity : 0.004 0.055 1361 Dihedral : 31.321 89.162 4224 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 11.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.05 % Allowed : 19.21 % Favored : 78.74 % 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: 2.52 (0.31), residues: 746 helix: 2.37 (0.22), residues: 551 sheet: None (None), residues: 0 loop : -0.39 (0.41), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS H 106 PHE 0.005 0.001 PHE G 25 TYR 0.032 0.001 TYR F 88 ARG 0.004 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 141 time to evaluate : 1.024 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8981 (tm-30) cc_final: 0.8585 (tm-30) REVERT: A 120 MET cc_start: 0.8802 (mmm) cc_final: 0.8572 (mmm) REVERT: B 53 GLU cc_start: 0.9086 (mp0) cc_final: 0.8568 (mp0) REVERT: B 63 GLU cc_start: 0.8933 (OUTLIER) cc_final: 0.8592 (mp0) REVERT: B 74 GLU cc_start: 0.8450 (mt-10) cc_final: 0.8163 (mt-10) REVERT: B 84 MET cc_start: 0.9366 (mmm) cc_final: 0.8975 (mmm) REVERT: B 88 TYR cc_start: 0.9052 (m-10) cc_final: 0.8702 (m-10) REVERT: C 36 LYS cc_start: 0.9596 (ttmt) cc_final: 0.9388 (ttmm) REVERT: C 56 GLU cc_start: 0.8594 (tt0) cc_final: 0.8374 (mm-30) REVERT: C 61 GLU cc_start: 0.8849 (OUTLIER) cc_final: 0.8571 (mm-30) REVERT: E 109 LEU cc_start: 0.9615 (tp) cc_final: 0.9281 (tp) REVERT: E 120 MET cc_start: 0.7780 (mpp) cc_final: 0.7290 (mpp) REVERT: F 53 GLU cc_start: 0.9257 (mp0) cc_final: 0.8755 (mp0) REVERT: F 84 MET cc_start: 0.9017 (tpp) cc_final: 0.8771 (tpp) REVERT: F 88 TYR cc_start: 0.8783 (m-80) cc_final: 0.7518 (m-80) REVERT: G 36 LYS cc_start: 0.9086 (mtmm) cc_final: 0.8778 (mtmm) REVERT: G 104 GLN cc_start: 0.8865 (mp10) cc_final: 0.8493 (pm20) REVERT: H 73 GLU cc_start: 0.9264 (tp30) cc_final: 0.8843 (tp30) outliers start: 13 outliers final: 5 residues processed: 147 average time/residue: 0.2223 time to fit residues: 48.3347 Evaluate side-chains 130 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 123 time to evaluate : 0.933 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 40 optimal weight: 8.9990 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 5.9990 chunk 33 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 31 HIS F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8696 moved from start: 0.6088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 13264 Z= 0.319 Angle : 0.659 15.000 19238 Z= 0.377 Chirality : 0.037 0.197 2184 Planarity : 0.005 0.054 1361 Dihedral : 32.020 89.563 4224 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 15.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.15 % Allowed : 21.89 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.44 (0.31), residues: 746 helix: 2.39 (0.23), residues: 545 sheet: None (None), residues: 0 loop : -0.59 (0.40), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.011 0.002 PHE F 100 TYR 0.028 0.002 TYR F 88 ARG 0.006 0.001 ARG G 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 116 time to evaluate : 1.033 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8957 (tm-30) cc_final: 0.8643 (tm-30) REVERT: A 120 MET cc_start: 0.8947 (mmm) cc_final: 0.8707 (mmm) REVERT: B 53 GLU cc_start: 0.9132 (mp0) cc_final: 0.8669 (mp0) REVERT: B 74 GLU cc_start: 0.8550 (mt-10) cc_final: 0.8243 (mt-10) REVERT: B 84 MET cc_start: 0.9288 (mmm) cc_final: 0.8905 (mmm) REVERT: B 88 TYR cc_start: 0.9131 (m-10) cc_final: 0.8766 (m-10) REVERT: C 36 LYS cc_start: 0.9622 (ttmt) cc_final: 0.9386 (ttmm) REVERT: C 61 GLU cc_start: 0.8856 (OUTLIER) cc_final: 0.8588 (mp0) REVERT: E 62 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8856 (pt) REVERT: E 65 LEU cc_start: 0.9874 (OUTLIER) cc_final: 0.9566 (mm) REVERT: E 120 MET cc_start: 0.8007 (mpp) cc_final: 0.7760 (mpp) REVERT: F 53 GLU cc_start: 0.9281 (mp0) cc_final: 0.9061 (mp0) REVERT: F 59 LYS cc_start: 0.9522 (tttm) cc_final: 0.8835 (tptm) REVERT: F 63 GLU cc_start: 0.9253 (mt-10) cc_final: 0.8596 (mt-10) REVERT: F 88 TYR cc_start: 0.8705 (m-80) cc_final: 0.8135 (m-80) REVERT: G 36 LYS cc_start: 0.9144 (mtmm) cc_final: 0.8928 (mtmm) REVERT: G 61 GLU cc_start: 0.8993 (mm-30) cc_final: 0.8793 (mm-30) REVERT: G 64 GLU cc_start: 0.9446 (OUTLIER) cc_final: 0.9074 (pp20) REVERT: G 104 GLN cc_start: 0.8960 (mp10) cc_final: 0.8536 (pm20) REVERT: H 80 TYR cc_start: 0.7363 (m-10) cc_final: 0.7042 (m-10) outliers start: 20 outliers final: 12 residues processed: 126 average time/residue: 0.2602 time to fit residues: 47.6094 Evaluate side-chains 121 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 105 time to evaluate : 0.960 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 66 ILE Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 87 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 32 optimal weight: 0.9980 chunk 51 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 0.0470 chunk 56 optimal weight: 4.9990 overall best weight: 0.9880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 25 ASN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 27 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8638 moved from start: 0.6165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 13264 Z= 0.191 Angle : 0.609 12.082 19238 Z= 0.349 Chirality : 0.034 0.170 2184 Planarity : 0.004 0.052 1361 Dihedral : 31.508 89.210 4224 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Rotamer: Outliers : 2.20 % Allowed : 22.83 % Favored : 74.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.31), residues: 746 helix: 2.41 (0.23), residues: 550 sheet: None (None), residues: 0 loop : -0.73 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.038 0.002 PHE E 67 TYR 0.028 0.001 TYR F 88 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 127 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8978 (tm-30) cc_final: 0.8602 (tm-30) REVERT: A 120 MET cc_start: 0.8984 (mmm) cc_final: 0.8689 (mmm) REVERT: B 53 GLU cc_start: 0.9038 (mp0) cc_final: 0.8534 (mp0) REVERT: B 63 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8615 (mp0) REVERT: B 84 MET cc_start: 0.9304 (mmm) cc_final: 0.8981 (mmm) REVERT: B 88 TYR cc_start: 0.9074 (m-10) cc_final: 0.8692 (m-10) REVERT: C 36 LYS cc_start: 0.9615 (ttmt) cc_final: 0.9399 (ttmm) REVERT: C 38 ASN cc_start: 0.9381 (m110) cc_final: 0.8732 (t0) REVERT: C 56 GLU cc_start: 0.8588 (tt0) cc_final: 0.8216 (mm-30) REVERT: C 61 GLU cc_start: 0.8819 (OUTLIER) cc_final: 0.8522 (mm-30) REVERT: E 105 GLU cc_start: 0.8955 (tp30) cc_final: 0.8715 (tm-30) REVERT: E 120 MET cc_start: 0.8108 (mpp) cc_final: 0.7906 (mtt) REVERT: F 53 GLU cc_start: 0.9286 (mp0) cc_final: 0.9018 (mp0) REVERT: F 59 LYS cc_start: 0.9498 (tttm) cc_final: 0.8686 (tptm) REVERT: F 63 GLU cc_start: 0.9265 (mt-10) cc_final: 0.8529 (mt-10) REVERT: F 88 TYR cc_start: 0.8551 (m-80) cc_final: 0.7797 (m-80) REVERT: G 36 LYS cc_start: 0.9118 (mtmm) cc_final: 0.8634 (mtmm) REVERT: G 56 GLU cc_start: 0.8879 (mt-10) cc_final: 0.8389 (mm-30) REVERT: G 64 GLU cc_start: 0.9359 (tm-30) cc_final: 0.9146 (pp20) REVERT: G 104 GLN cc_start: 0.8964 (mp10) cc_final: 0.8749 (pm20) REVERT: H 80 TYR cc_start: 0.7118 (m-10) cc_final: 0.6669 (m-10) outliers start: 14 outliers final: 7 residues processed: 134 average time/residue: 0.2257 time to fit residues: 44.4100 Evaluate side-chains 128 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 119 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.6456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13264 Z= 0.219 Angle : 0.610 12.263 19238 Z= 0.350 Chirality : 0.034 0.222 2184 Planarity : 0.004 0.042 1361 Dihedral : 31.521 87.765 4224 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 12.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 2.05 % Allowed : 24.25 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.55 (0.31), residues: 746 helix: 2.48 (0.23), residues: 543 sheet: None (None), residues: 0 loop : -0.56 (0.41), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS A 113 PHE 0.026 0.001 PHE E 67 TYR 0.019 0.001 TYR F 88 ARG 0.002 0.000 ARG G 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 121 time to evaluate : 1.001 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8599 (tm-30) REVERT: B 53 GLU cc_start: 0.8975 (mp0) cc_final: 0.8465 (mp0) REVERT: B 84 MET cc_start: 0.9306 (mmm) cc_final: 0.8979 (mmm) REVERT: B 88 TYR cc_start: 0.9042 (m-10) cc_final: 0.8655 (m-10) REVERT: C 36 LYS cc_start: 0.9628 (ttmt) cc_final: 0.9399 (ttmm) REVERT: C 38 ASN cc_start: 0.9334 (m110) cc_final: 0.8750 (t0) REVERT: C 56 GLU cc_start: 0.8574 (tt0) cc_final: 0.8210 (mm-30) REVERT: C 61 GLU cc_start: 0.8798 (OUTLIER) cc_final: 0.8498 (mp0) REVERT: E 65 LEU cc_start: 0.9832 (OUTLIER) cc_final: 0.9567 (mm) REVERT: E 105 GLU cc_start: 0.8985 (tp30) cc_final: 0.8728 (tm-30) REVERT: E 120 MET cc_start: 0.8082 (mpp) cc_final: 0.7829 (mtt) REVERT: F 53 GLU cc_start: 0.9333 (mp0) cc_final: 0.9008 (mp0) REVERT: F 59 LYS cc_start: 0.9488 (tttm) cc_final: 0.8384 (tptm) REVERT: F 63 GLU cc_start: 0.9263 (mt-10) cc_final: 0.8582 (mp0) REVERT: F 88 TYR cc_start: 0.8801 (m-80) cc_final: 0.7782 (m-80) REVERT: G 36 LYS cc_start: 0.9140 (mtmm) cc_final: 0.8895 (mtmm) REVERT: G 64 GLU cc_start: 0.9408 (tm-30) cc_final: 0.9206 (pp20) REVERT: H 73 GLU cc_start: 0.9241 (tp30) cc_final: 0.8708 (tp30) outliers start: 13 outliers final: 7 residues processed: 129 average time/residue: 0.2215 time to fit residues: 42.1389 Evaluate side-chains 125 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 116 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 7.9990 chunk 62 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 48 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 8.9990 chunk 94 optimal weight: 6.9990 chunk 85 optimal weight: 8.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 1.9990 overall best weight: 2.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.6960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13264 Z= 0.272 Angle : 0.641 11.216 19238 Z= 0.366 Chirality : 0.035 0.215 2184 Planarity : 0.004 0.045 1361 Dihedral : 31.738 88.449 4224 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.36 % Allowed : 25.04 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.31), residues: 746 helix: 2.41 (0.23), residues: 549 sheet: None (None), residues: 0 loop : -0.70 (0.42), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS B 75 PHE 0.033 0.002 PHE E 67 TYR 0.021 0.002 TYR F 88 ARG 0.004 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 119 time to evaluate : 0.785 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9463 (pt0) cc_final: 0.9234 (pp20) REVERT: A 105 GLU cc_start: 0.8940 (tm-30) cc_final: 0.8622 (tm-30) REVERT: B 53 GLU cc_start: 0.8989 (mp0) cc_final: 0.8518 (mp0) REVERT: B 59 LYS cc_start: 0.9161 (tppp) cc_final: 0.8657 (tppt) REVERT: B 63 GLU cc_start: 0.8922 (OUTLIER) cc_final: 0.8585 (mp0) REVERT: B 84 MET cc_start: 0.9290 (mmm) cc_final: 0.8936 (mmm) REVERT: B 88 TYR cc_start: 0.9068 (m-10) cc_final: 0.8626 (m-10) REVERT: C 36 LYS cc_start: 0.9637 (ttmt) cc_final: 0.9394 (ttmm) REVERT: C 38 ASN cc_start: 0.9347 (m110) cc_final: 0.8762 (t0) REVERT: C 61 GLU cc_start: 0.8804 (OUTLIER) cc_final: 0.8521 (mp0) REVERT: E 65 LEU cc_start: 0.9841 (OUTLIER) cc_final: 0.9574 (mm) REVERT: E 105 GLU cc_start: 0.9001 (tp30) cc_final: 0.8766 (tm-30) REVERT: E 120 MET cc_start: 0.8037 (mpp) cc_final: 0.7733 (mtt) REVERT: F 53 GLU cc_start: 0.9362 (mp0) cc_final: 0.9010 (mp0) REVERT: F 88 TYR cc_start: 0.8708 (m-80) cc_final: 0.8474 (m-80) REVERT: G 36 LYS cc_start: 0.9164 (mtmm) cc_final: 0.8695 (mtmm) REVERT: G 56 GLU cc_start: 0.8838 (mt-10) cc_final: 0.8276 (mm-30) REVERT: H 80 TYR cc_start: 0.7311 (m-10) cc_final: 0.6934 (m-10) REVERT: H 106 HIS cc_start: 0.9155 (OUTLIER) cc_final: 0.8762 (m90) outliers start: 15 outliers final: 10 residues processed: 129 average time/residue: 0.2305 time to fit residues: 43.5934 Evaluate side-chains 125 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 106 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 3.9990 chunk 71 optimal weight: 0.9980 chunk 28 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 86 optimal weight: 10.0000 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 0.9980 chunk 96 optimal weight: 7.9990 chunk 59 optimal weight: 5.9990 chunk 45 optimal weight: 0.9980 chunk 67 optimal weight: 0.8980 overall best weight: 1.5782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.7132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13264 Z= 0.221 Angle : 0.629 11.871 19238 Z= 0.359 Chirality : 0.034 0.204 2184 Planarity : 0.004 0.048 1361 Dihedral : 31.440 88.008 4224 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.89 % Allowed : 25.98 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.49 (0.31), residues: 746 helix: 2.43 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.67 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS A 113 PHE 0.041 0.002 PHE E 67 TYR 0.017 0.001 TYR F 88 ARG 0.003 0.000 ARG F 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 121 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9460 (pt0) cc_final: 0.9239 (pp20) REVERT: A 105 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8587 (tm-30) REVERT: A 120 MET cc_start: 0.8875 (mmm) cc_final: 0.8176 (mmm) REVERT: B 53 GLU cc_start: 0.8919 (mp0) cc_final: 0.8482 (mp0) REVERT: B 59 LYS cc_start: 0.9106 (tppp) cc_final: 0.8618 (ttmm) REVERT: B 63 GLU cc_start: 0.8923 (OUTLIER) cc_final: 0.8591 (mp0) REVERT: B 84 MET cc_start: 0.9338 (mmm) cc_final: 0.9005 (mmm) REVERT: B 88 TYR cc_start: 0.9044 (m-10) cc_final: 0.8649 (m-10) REVERT: C 36 LYS cc_start: 0.9630 (ttmt) cc_final: 0.9376 (ttmm) REVERT: C 38 ASN cc_start: 0.9310 (m110) cc_final: 0.8767 (t0) REVERT: C 56 GLU cc_start: 0.8587 (tt0) cc_final: 0.8132 (mm-30) REVERT: C 61 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8478 (mp0) REVERT: E 50 GLU cc_start: 0.9409 (pt0) cc_final: 0.9186 (pp20) REVERT: E 65 LEU cc_start: 0.9821 (OUTLIER) cc_final: 0.9542 (mm) REVERT: E 105 GLU cc_start: 0.8997 (tp30) cc_final: 0.8768 (tm-30) REVERT: E 120 MET cc_start: 0.8075 (mpp) cc_final: 0.7751 (mtt) REVERT: F 53 GLU cc_start: 0.9375 (mp0) cc_final: 0.8993 (mp0) REVERT: F 63 GLU cc_start: 0.9225 (mt-10) cc_final: 0.8546 (mt-10) REVERT: F 88 TYR cc_start: 0.8603 (m-80) cc_final: 0.8325 (m-80) REVERT: G 36 LYS cc_start: 0.9156 (mtmm) cc_final: 0.8677 (mtmm) REVERT: G 56 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8394 (mm-30) REVERT: H 73 GLU cc_start: 0.9228 (tp30) cc_final: 0.8681 (tp30) REVERT: H 80 TYR cc_start: 0.7326 (m-10) cc_final: 0.6877 (m-10) REVERT: H 106 HIS cc_start: 0.9115 (OUTLIER) cc_final: 0.8722 (m90) outliers start: 12 outliers final: 6 residues processed: 129 average time/residue: 0.2258 time to fit residues: 42.7508 Evaluate side-chains 126 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 106 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 0.6980 chunk 62 optimal weight: 0.7980 chunk 49 optimal weight: 0.9980 chunk 64 optimal weight: 4.9990 chunk 86 optimal weight: 10.0000 chunk 24 optimal weight: 0.9990 chunk 74 optimal weight: 8.9990 chunk 11 optimal weight: 10.0000 overall best weight: 1.6984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.7307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 13264 Z= 0.228 Angle : 0.637 12.870 19238 Z= 0.361 Chirality : 0.034 0.201 2184 Planarity : 0.004 0.048 1361 Dihedral : 31.484 88.056 4224 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 12.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.89 % Allowed : 25.51 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.31), residues: 746 helix: 2.41 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.64 (0.43), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 75 PHE 0.048 0.002 PHE E 67 TYR 0.017 0.001 TYR F 88 ARG 0.003 0.000 ARG F 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 116 time to evaluate : 0.802 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.9450 (pt0) cc_final: 0.9249 (pp20) REVERT: A 105 GLU cc_start: 0.8942 (tm-30) cc_final: 0.8618 (tm-30) REVERT: A 120 MET cc_start: 0.8881 (mmm) cc_final: 0.8162 (mmm) REVERT: B 53 GLU cc_start: 0.8924 (mp0) cc_final: 0.8483 (mp0) REVERT: B 59 LYS cc_start: 0.9125 (tppp) cc_final: 0.8671 (ttmm) REVERT: B 63 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8623 (mp0) REVERT: B 84 MET cc_start: 0.9305 (mmm) cc_final: 0.8969 (mmm) REVERT: B 88 TYR cc_start: 0.9040 (m-10) cc_final: 0.8623 (m-10) REVERT: C 38 ASN cc_start: 0.9326 (m110) cc_final: 0.8824 (t0) REVERT: C 61 GLU cc_start: 0.8796 (OUTLIER) cc_final: 0.8492 (mp0) REVERT: E 50 GLU cc_start: 0.9394 (pt0) cc_final: 0.9154 (pp20) REVERT: E 120 MET cc_start: 0.8058 (mpp) cc_final: 0.7732 (mtt) REVERT: F 53 GLU cc_start: 0.9404 (mp0) cc_final: 0.9037 (mp0) REVERT: F 63 GLU cc_start: 0.9202 (mt-10) cc_final: 0.8294 (mt-10) REVERT: F 88 TYR cc_start: 0.8650 (m-80) cc_final: 0.8330 (m-80) REVERT: G 36 LYS cc_start: 0.9165 (mtmm) cc_final: 0.8686 (mtmm) REVERT: G 56 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8386 (mm-30) REVERT: H 73 GLU cc_start: 0.9238 (tp30) cc_final: 0.8600 (tp30) REVERT: H 80 TYR cc_start: 0.7216 (m-10) cc_final: 0.6792 (m-10) REVERT: H 106 HIS cc_start: 0.9158 (OUTLIER) cc_final: 0.8760 (m90) outliers start: 12 outliers final: 7 residues processed: 125 average time/residue: 0.2296 time to fit residues: 41.5762 Evaluate side-chains 123 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 113 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 106 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 1.9990 chunk 81 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 83 optimal weight: 7.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 4 optimal weight: 6.9990 chunk 58 optimal weight: 7.9990 chunk 92 optimal weight: 7.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** 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 = 0.3052 r_free = 0.3052 target = 0.036056 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2585 r_free = 0.2585 target = 0.025322 restraints weight = 120006.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2621 r_free = 0.2621 target = 0.025861 restraints weight = 57508.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2644 r_free = 0.2644 target = 0.026225 restraints weight = 36226.683| |-----------------------------------------------------------------------------| r_work (final): 0.2590 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8712 moved from start: 0.7597 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13264 Z= 0.267 Angle : 0.655 12.228 19238 Z= 0.373 Chirality : 0.034 0.196 2184 Planarity : 0.004 0.047 1361 Dihedral : 31.628 88.965 4224 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 13.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 1.89 % Allowed : 25.98 % Favored : 72.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.46 (0.31), residues: 746 helix: 2.41 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.69 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.051 0.002 PHE E 67 TYR 0.016 0.002 TYR H 80 ARG 0.003 0.000 ARG A 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1973.37 seconds wall clock time: 36 minutes 50.91 seconds (2210.91 seconds total)