Starting phenix.real_space_refine on Fri Jul 19 00:05:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2024/8sza_40905.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2024/8sza_40905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2024/8sza_40905.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2024/8sza_40905.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2024/8sza_40905.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sza_40905/07_2024/8sza_40905.cif" } resolution = 2.75 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= 0.001 sd= 0.025 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: 4 Type Number sf(0) Gaussians S 12 5.16 5 C 3258 2.51 5 N 726 2.21 5 O 804 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 69": "OE1" <-> "OE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 116": "OD1" <-> "OD2" Residue "C TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 49": "OE1" <-> "OE2" Residue "D ASP 53": "OD1" <-> "OD2" Residue "E ASP 53": "OD1" <-> "OD2" Residue "E PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 49": "OE1" <-> "OE2" Residue "F ASP 53": "OD1" <-> "OD2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4800 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "C" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "D" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "E" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "F" Number of atoms: 772 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 772 Classifications: {'peptide': 101} Link IDs: {'PTRANS': 3, 'TRANS': 97} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Chain: "E" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 56 Unusual residues: {'CLR': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "F" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.62, per 1000 atoms: 0.75 Number of scatterers: 4800 At special positions: 0 Unit cell: (56.76, 70.62, 94.38, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 12 16.00 O 804 8.00 N 726 7.00 C 3258 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: 1.84 Conformation dependent library (CDL) restraints added in 853.3 milliseconds 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1164 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 0 sheets defined 88.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'A' and resid 40 through 50 Processing helix chain 'A' and resid 54 through 71 removed outlier: 3.517A pdb=" N GLY A 71 " --> pdb=" O VAL A 67 " (cutoff:3.500A) Processing helix chain 'A' and resid 76 through 103 removed outlier: 4.120A pdb=" N LYS A 103 " --> pdb=" O ILE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 108 removed outlier: 4.005A pdb=" N ASN A 108 " --> pdb=" O TYR A 104 " (cutoff:3.500A) Processing helix chain 'A' and resid 111 through 139 Processing helix chain 'B' and resid 40 through 50 Processing helix chain 'B' and resid 54 through 71 removed outlier: 3.572A pdb=" N GLY B 71 " --> pdb=" O VAL B 67 " (cutoff:3.500A) Processing helix chain 'B' and resid 76 through 107 removed outlier: 4.175A pdb=" N LYS B 103 " --> pdb=" O ILE B 99 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N TYR B 104 " --> pdb=" O PHE B 100 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N ASP B 105 " --> pdb=" O LEU B 101 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LEU B 106 " --> pdb=" O VAL B 102 " (cutoff:3.500A) Processing helix chain 'B' and resid 111 through 139 Processing helix chain 'C' and resid 40 through 50 removed outlier: 3.506A pdb=" N SER C 50 " --> pdb=" O SER C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 54 through 71 Processing helix chain 'C' and resid 76 through 102 Processing helix chain 'C' and resid 111 through 139 Processing helix chain 'D' and resid 40 through 50 Processing helix chain 'D' and resid 54 through 71 removed outlier: 3.744A pdb=" N MET D 58 " --> pdb=" O ILE D 54 " (cutoff:3.500A) removed outlier: 3.569A pdb=" N GLY D 71 " --> pdb=" O VAL D 67 " (cutoff:3.500A) Processing helix chain 'D' and resid 76 through 107 removed outlier: 3.512A pdb=" N VAL D 102 " --> pdb=" O LEU D 98 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N LYS D 103 " --> pdb=" O ILE D 99 " (cutoff:3.500A) removed outlier: 4.366A pdb=" N TYR D 104 " --> pdb=" O PHE D 100 " (cutoff:3.500A) removed outlier: 3.753A pdb=" N LEU D 106 " --> pdb=" O VAL D 102 " (cutoff:3.500A) Processing helix chain 'D' and resid 111 through 139 removed outlier: 3.643A pdb=" N PHE D 135 " --> pdb=" O VAL D 131 " (cutoff:3.500A) Processing helix chain 'E' and resid 40 through 50 Processing helix chain 'E' and resid 54 through 71 removed outlier: 3.660A pdb=" N GLY E 71 " --> pdb=" O VAL E 67 " (cutoff:3.500A) Processing helix chain 'E' and resid 76 through 103 removed outlier: 4.151A pdb=" N LYS E 103 " --> pdb=" O ILE E 99 " (cutoff:3.500A) Processing helix chain 'E' and resid 103 through 108 removed outlier: 3.667A pdb=" N ASN E 108 " --> pdb=" O TYR E 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 111 through 139 Processing helix chain 'F' and resid 40 through 50 Processing helix chain 'F' and resid 54 through 71 removed outlier: 3.500A pdb=" N GLY F 71 " --> pdb=" O VAL F 67 " (cutoff:3.500A) Processing helix chain 'F' and resid 76 through 102 Processing helix chain 'F' and resid 111 through 139 410 hydrogen bonds defined for protein. 1230 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.23 Time building geometry restraints manager: 2.03 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1416 1.35 - 1.46: 1057 1.46 - 1.58: 2405 1.58 - 1.70: 0 1.70 - 1.82: 24 Bond restraints: 4902 Sorted by residual: bond pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 1.520 1.563 -0.043 3.00e-02 1.11e+03 2.06e+00 bond pdb=" CA PHE C 74 " pdb=" CB PHE C 74 " ideal model delta sigma weight residual 1.528 1.507 0.021 1.58e-02 4.01e+03 1.70e+00 bond pdb=" CD2 HIS F 112 " pdb=" NE2 HIS F 112 " ideal model delta sigma weight residual 1.374 1.360 0.014 1.10e-02 8.26e+03 1.61e+00 bond pdb=" CA HIS F 112 " pdb=" CB HIS F 112 " ideal model delta sigma weight residual 1.528 1.510 0.019 1.59e-02 3.96e+03 1.39e+00 bond pdb=" CG HIS F 112 " pdb=" ND1 HIS F 112 " ideal model delta sigma weight residual 1.378 1.390 -0.012 1.10e-02 8.26e+03 1.28e+00 ... (remaining 4897 not shown) Histogram of bond angle deviations from ideal: 99.31 - 105.72: 97 105.72 - 112.14: 2731 112.14 - 118.55: 1316 118.55 - 124.97: 2528 124.97 - 131.39: 36 Bond angle restraints: 6708 Sorted by residual: angle pdb=" CB MET A 51 " pdb=" CG MET A 51 " pdb=" SD MET A 51 " ideal model delta sigma weight residual 112.70 123.47 -10.77 3.00e+00 1.11e-01 1.29e+01 angle pdb=" CA MET A 58 " pdb=" CB MET A 58 " pdb=" CG MET A 58 " ideal model delta sigma weight residual 114.10 120.87 -6.77 2.00e+00 2.50e-01 1.14e+01 angle pdb=" CA GLU A 69 " pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " ideal model delta sigma weight residual 114.10 120.83 -6.73 2.00e+00 2.50e-01 1.13e+01 angle pdb=" C TYR D 77 " pdb=" N VAL D 78 " pdb=" CA VAL D 78 " ideal model delta sigma weight residual 120.33 122.84 -2.51 8.00e-01 1.56e+00 9.83e+00 angle pdb=" CB GLU A 69 " pdb=" CG GLU A 69 " pdb=" CD GLU A 69 " ideal model delta sigma weight residual 112.60 117.81 -5.21 1.70e+00 3.46e-01 9.41e+00 ... (remaining 6703 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.55: 2792 16.55 - 33.09: 284 33.09 - 49.64: 88 49.64 - 66.19: 27 66.19 - 82.73: 1 Dihedral angle restraints: 3192 sinusoidal: 1410 harmonic: 1782 Sorted by residual: dihedral pdb=" CG LYS B 65 " pdb=" CD LYS B 65 " pdb=" CE LYS B 65 " pdb=" NZ LYS B 65 " ideal model delta sinusoidal sigma weight residual -60.00 -2.88 -57.12 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG LYS B 103 " pdb=" CD LYS B 103 " pdb=" CE LYS B 103 " pdb=" NZ LYS B 103 " ideal model delta sinusoidal sigma weight residual 180.00 122.94 57.06 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" N MET E 51 " pdb=" CA MET E 51 " pdb=" CB MET E 51 " pdb=" CG MET E 51 " ideal model delta sinusoidal sigma weight residual -180.00 -123.30 -56.70 3 1.50e+01 4.44e-03 9.41e+00 ... (remaining 3189 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 454 0.021 - 0.042: 244 0.042 - 0.063: 109 0.063 - 0.084: 45 0.084 - 0.104: 18 Chirality restraints: 870 Sorted by residual: chirality pdb=" CB VAL A 67 " pdb=" CA VAL A 67 " pdb=" CG1 VAL A 67 " pdb=" CG2 VAL A 67 " both_signs ideal model delta sigma weight residual False -2.63 -2.52 -0.10 2.00e-01 2.50e+01 2.73e-01 chirality pdb=" CA PRO F 79 " pdb=" N PRO F 79 " pdb=" C PRO F 79 " pdb=" CB PRO F 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.48e-01 chirality pdb=" CA PRO C 79 " pdb=" N PRO C 79 " pdb=" C PRO C 79 " pdb=" CB PRO C 79 " both_signs ideal model delta sigma weight residual False 2.72 2.62 0.10 2.00e-01 2.50e+01 2.42e-01 ... (remaining 867 not shown) Planarity restraints: 780 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 127 " -0.013 2.00e-02 2.50e+03 1.72e-02 5.18e+00 pdb=" CG PHE A 127 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE A 127 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 PHE A 127 " -0.015 2.00e-02 2.50e+03 pdb=" CE1 PHE A 127 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 PHE A 127 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 127 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 69 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.50e+00 pdb=" CD GLU A 69 " 0.037 2.00e-02 2.50e+03 pdb=" OE1 GLU A 69 " -0.013 2.00e-02 2.50e+03 pdb=" OE2 GLU A 69 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP F 53 " -0.006 2.00e-02 2.50e+03 1.29e-02 1.66e+00 pdb=" CG ASP F 53 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASP F 53 " -0.008 2.00e-02 2.50e+03 pdb=" OD2 ASP F 53 " -0.008 2.00e-02 2.50e+03 ... (remaining 777 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 184 2.73 - 3.27: 5207 3.27 - 3.81: 7791 3.81 - 4.36: 8925 4.36 - 4.90: 15072 Nonbonded interactions: 37179 Sorted by model distance: nonbonded pdb=" O MET D 58 " pdb=" OG SER D 62 " model vdw 2.185 2.440 nonbonded pdb=" OH TYR F 104 " pdb=" O1 CLR F 201 " model vdw 2.196 2.440 nonbonded pdb=" O MET E 58 " pdb=" OG SER E 62 " model vdw 2.225 2.440 nonbonded pdb=" OD1 ASN D 120 " pdb=" NZ LYS E 103 " model vdw 2.351 2.520 nonbonded pdb=" O MET F 58 " pdb=" OG SER F 62 " model vdw 2.414 2.440 ... (remaining 37174 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 'B' and resid 39 through 139) selection = (chain 'C' and resid 39 through 139) selection = (chain 'D' and resid 39 through 139) selection = (chain 'E' and resid 39 through 139) selection = (chain 'F' and resid 39 through 139) } 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.620 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 17.390 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.030 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:12.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.960 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 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 : 0.003 0.043 4902 Z= 0.203 Angle : 0.652 10.766 6708 Z= 0.325 Chirality : 0.033 0.104 870 Planarity : 0.002 0.022 780 Dihedral : 15.140 82.732 2028 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 8.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 0.98 % Allowed : 20.98 % Favored : 78.04 % 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: 2.12 (0.35), residues: 594 helix: 1.96 (0.23), residues: 492 sheet: None (None), residues: 0 loop : -1.39 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.039 0.001 PHE A 127 TYR 0.009 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.515 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 44 LYS cc_start: 0.6964 (mmtt) cc_final: 0.5977 (tmtt) outliers start: 5 outliers final: 5 residues processed: 90 average time/residue: 0.7231 time to fit residues: 69.0864 Evaluate side-chains 89 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 ILE Chi-restraints excluded: chain C residue 102 VAL Chi-restraints excluded: chain C residue 128 ILE Chi-restraints excluded: chain F residue 52 LEU Chi-restraints excluded: chain F residue 54 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 30 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 54 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4902 Z= 0.195 Angle : 0.541 6.732 6708 Z= 0.272 Chirality : 0.036 0.134 870 Planarity : 0.003 0.016 780 Dihedral : 9.488 50.575 1017 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 2.35 % Allowed : 19.02 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.00 (0.35), residues: 594 helix: 2.50 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.19 (0.76), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.000 HIS B 112 PHE 0.019 0.002 PHE F 127 TYR 0.011 0.001 TYR D 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 0.544 Fit side-chains REVERT: A 58 MET cc_start: 0.8025 (mpt) cc_final: 0.7661 (mpt) REVERT: A 104 TYR cc_start: 0.7988 (OUTLIER) cc_final: 0.6269 (t80) REVERT: B 58 MET cc_start: 0.7336 (mtp) cc_final: 0.7085 (mtm) REVERT: D 44 LYS cc_start: 0.7079 (mmtt) cc_final: 0.6089 (tmtt) outliers start: 12 outliers final: 5 residues processed: 99 average time/residue: 0.6548 time to fit residues: 69.2695 Evaluate side-chains 91 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 10.0000 chunk 16 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 54 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 43 optimal weight: 0.4980 chunk 53 optimal weight: 4.9990 overall best weight: 0.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7680 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4902 Z= 0.216 Angle : 0.536 6.786 6708 Z= 0.263 Chirality : 0.037 0.158 870 Planarity : 0.002 0.016 780 Dihedral : 9.375 50.609 1008 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 3.92 % Allowed : 19.41 % Favored : 76.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.04 (0.35), residues: 594 helix: 2.51 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -1.06 (0.78), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.020 0.002 PHE C 127 TYR 0.014 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 95 time to evaluate : 0.529 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7974 (mpt) cc_final: 0.7338 (mpt) REVERT: A 104 TYR cc_start: 0.7998 (OUTLIER) cc_final: 0.6293 (t80) REVERT: B 58 MET cc_start: 0.7382 (mtp) cc_final: 0.7098 (mtm) REVERT: C 70 GLN cc_start: 0.8286 (tt0) cc_final: 0.8080 (tp-100) REVERT: D 44 LYS cc_start: 0.7063 (mmtt) cc_final: 0.5952 (tmtt) REVERT: D 88 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7750 (mt) REVERT: D 101 LEU cc_start: 0.7845 (OUTLIER) cc_final: 0.7508 (tt) REVERT: E 88 LEU cc_start: 0.8316 (OUTLIER) cc_final: 0.8001 (tm) outliers start: 20 outliers final: 12 residues processed: 104 average time/residue: 0.6689 time to fit residues: 74.1833 Evaluate side-chains 101 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 85 time to evaluate : 0.516 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain E residue 73 SER Chi-restraints excluded: chain E residue 88 LEU Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 119 ASN ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7695 moved from start: 0.2220 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4902 Z= 0.220 Angle : 0.538 6.914 6708 Z= 0.263 Chirality : 0.037 0.138 870 Planarity : 0.002 0.016 780 Dihedral : 9.365 50.968 1008 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Rotamer: Outliers : 4.12 % Allowed : 20.00 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.35), residues: 594 helix: 2.59 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.76 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.031 0.002 PHE A 127 TYR 0.007 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 89 time to evaluate : 0.534 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7881 (mpt) cc_final: 0.7318 (mpt) REVERT: A 104 TYR cc_start: 0.8031 (OUTLIER) cc_final: 0.6371 (t80) REVERT: B 58 MET cc_start: 0.7473 (mtp) cc_final: 0.7172 (mtm) REVERT: D 44 LYS cc_start: 0.7091 (mmtt) cc_final: 0.5875 (tmtt) REVERT: D 58 MET cc_start: 0.8303 (mpt) cc_final: 0.8057 (mpt) REVERT: D 88 LEU cc_start: 0.8440 (OUTLIER) cc_final: 0.7750 (mt) outliers start: 21 outliers final: 11 residues processed: 102 average time/residue: 0.7041 time to fit residues: 76.7320 Evaluate side-chains 96 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 SER Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 99 ILE Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 23 optimal weight: 6.9990 chunk 49 optimal weight: 1.9990 chunk 40 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 19 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 60 ASN E 63 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4902 Z= 0.222 Angle : 0.548 7.997 6708 Z= 0.268 Chirality : 0.037 0.136 870 Planarity : 0.002 0.014 780 Dihedral : 9.374 50.761 1008 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 9.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 3.33 % Allowed : 21.37 % Favored : 75.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.36), residues: 594 helix: 2.55 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.83 (0.82), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS F 112 PHE 0.028 0.002 PHE A 127 TYR 0.006 0.001 TYR A 77 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 89 time to evaluate : 0.563 Fit side-chains REVERT: A 58 MET cc_start: 0.7866 (OUTLIER) cc_final: 0.7452 (mpt) REVERT: A 104 TYR cc_start: 0.8023 (OUTLIER) cc_final: 0.6371 (t80) REVERT: B 58 MET cc_start: 0.7489 (mtp) cc_final: 0.7281 (mtp) REVERT: B 115 LEU cc_start: 0.7602 (OUTLIER) cc_final: 0.7238 (tm) REVERT: B 119 ASN cc_start: 0.8173 (m-40) cc_final: 0.7810 (m-40) REVERT: D 44 LYS cc_start: 0.7086 (mmtt) cc_final: 0.5827 (tmtt) REVERT: D 45 LYS cc_start: 0.8216 (OUTLIER) cc_final: 0.8005 (tttm) REVERT: D 58 MET cc_start: 0.8208 (mpt) cc_final: 0.7944 (mpt) REVERT: D 88 LEU cc_start: 0.8412 (OUTLIER) cc_final: 0.7722 (mt) REVERT: D 101 LEU cc_start: 0.7873 (OUTLIER) cc_final: 0.7505 (tt) outliers start: 17 outliers final: 10 residues processed: 97 average time/residue: 0.7309 time to fit residues: 75.4302 Evaluate side-chains 98 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 45 LYS Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain D residue 137 THR Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.8980 chunk 58 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.0050 chunk 30 optimal weight: 10.0000 chunk 55 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 42 optimal weight: 2.9990 overall best weight: 1.1800 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 107 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 120 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7711 moved from start: 0.2512 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4902 Z= 0.233 Angle : 0.560 7.813 6708 Z= 0.272 Chirality : 0.037 0.155 870 Planarity : 0.002 0.015 780 Dihedral : 9.401 50.588 1008 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 3.73 % Allowed : 22.35 % Favored : 73.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.10 (0.36), residues: 594 helix: 2.52 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.80 (0.83), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.026 0.002 PHE F 127 TYR 0.006 0.001 TYR A 77 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 89 time to evaluate : 0.532 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7802 (OUTLIER) cc_final: 0.7381 (mpt) REVERT: A 104 TYR cc_start: 0.8010 (OUTLIER) cc_final: 0.6409 (t80) REVERT: B 58 MET cc_start: 0.7496 (mtp) cc_final: 0.7266 (mtp) REVERT: B 115 LEU cc_start: 0.7576 (OUTLIER) cc_final: 0.7196 (tm) REVERT: B 119 ASN cc_start: 0.8172 (m-40) cc_final: 0.7828 (m-40) REVERT: C 70 GLN cc_start: 0.8416 (tp-100) cc_final: 0.8125 (tp-100) REVERT: D 44 LYS cc_start: 0.7168 (mmtt) cc_final: 0.5849 (tmtt) REVERT: D 58 MET cc_start: 0.8108 (mpt) cc_final: 0.7858 (mpt) REVERT: D 88 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.7744 (mt) REVERT: D 101 LEU cc_start: 0.7855 (OUTLIER) cc_final: 0.7589 (tt) outliers start: 19 outliers final: 9 residues processed: 99 average time/residue: 0.7443 time to fit residues: 78.9396 Evaluate side-chains 95 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 81 time to evaluate : 0.577 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 104 TYR Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 102 VAL Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Chi-restraints excluded: chain F residue 137 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 23 optimal weight: 4.9990 chunk 34 optimal weight: 0.7980 chunk 17 optimal weight: 0.0270 chunk 11 optimal weight: 4.9990 chunk 39 optimal weight: 0.4980 overall best weight: 0.4438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7665 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4902 Z= 0.163 Angle : 0.535 8.738 6708 Z= 0.262 Chirality : 0.035 0.177 870 Planarity : 0.002 0.018 780 Dihedral : 9.154 48.742 1008 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Rotamer: Outliers : 2.75 % Allowed : 24.90 % Favored : 72.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.47 (0.36), residues: 594 helix: 2.79 (0.23), residues: 504 sheet: None (None), residues: 0 loop : -0.83 (0.81), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS E 40 PHE 0.031 0.001 PHE A 127 TYR 0.005 0.001 TYR A 77 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.575 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7688 (OUTLIER) cc_final: 0.7429 (mpt) REVERT: B 58 MET cc_start: 0.7480 (mtp) cc_final: 0.7245 (mtp) REVERT: B 119 ASN cc_start: 0.8233 (m-40) cc_final: 0.7899 (m-40) REVERT: C 70 GLN cc_start: 0.8432 (tp-100) cc_final: 0.8089 (tp-100) REVERT: D 44 LYS cc_start: 0.7114 (mmtt) cc_final: 0.5826 (tmtt) REVERT: D 88 LEU cc_start: 0.8390 (OUTLIER) cc_final: 0.7766 (mt) REVERT: D 101 LEU cc_start: 0.7932 (OUTLIER) cc_final: 0.7592 (tt) outliers start: 14 outliers final: 9 residues processed: 97 average time/residue: 0.6970 time to fit residues: 72.1252 Evaluate side-chains 97 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 MET Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain B residue 74 PHE Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 62 SER Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 45 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 53 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 42 optimal weight: 6.9990 chunk 16 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7699 moved from start: 0.2648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4902 Z= 0.221 Angle : 0.577 8.803 6708 Z= 0.281 Chirality : 0.038 0.173 870 Planarity : 0.002 0.020 780 Dihedral : 9.232 48.983 1008 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.35 % Allowed : 26.27 % Favored : 71.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.35), residues: 594 helix: 2.61 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.69 (0.76), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.032 0.002 PHE A 127 TYR 0.012 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.545 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7757 (OUTLIER) cc_final: 0.7400 (mpt) REVERT: B 58 MET cc_start: 0.7497 (mtp) cc_final: 0.7252 (mtp) REVERT: B 119 ASN cc_start: 0.8296 (m-40) cc_final: 0.7943 (m-40) REVERT: C 70 GLN cc_start: 0.8456 (tp-100) cc_final: 0.8079 (tp-100) REVERT: D 44 LYS cc_start: 0.7151 (mmtt) cc_final: 0.5798 (tmtt) REVERT: D 88 LEU cc_start: 0.8413 (OUTLIER) cc_final: 0.7756 (mt) REVERT: D 101 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7559 (tt) REVERT: F 69 GLU cc_start: 0.8178 (pt0) cc_final: 0.7947 (pt0) outliers start: 12 outliers final: 7 residues processed: 90 average time/residue: 0.7380 time to fit residues: 70.7749 Evaluate side-chains 92 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 82 time to evaluate : 0.544 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 35 optimal weight: 0.6980 chunk 56 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 27 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 59 optimal weight: 0.0470 chunk 55 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7663 moved from start: 0.2675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4902 Z= 0.173 Angle : 0.568 9.543 6708 Z= 0.278 Chirality : 0.036 0.192 870 Planarity : 0.002 0.019 780 Dihedral : 9.077 49.590 1008 Min Nonbonded Distance : 2.249 Molprobity Statistics. All-atom Clashscore : 10.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.16 % Allowed : 27.45 % Favored : 70.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.43 (0.36), residues: 594 helix: 2.79 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.73 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 112 PHE 0.034 0.001 PHE A 127 TYR 0.008 0.001 TYR B 77 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 92 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7662 (OUTLIER) cc_final: 0.7420 (mpt) REVERT: B 58 MET cc_start: 0.7500 (mtp) cc_final: 0.7190 (mtm) REVERT: B 119 ASN cc_start: 0.8284 (m-40) cc_final: 0.7941 (m-40) REVERT: C 70 GLN cc_start: 0.8453 (tp-100) cc_final: 0.8078 (tp-100) REVERT: D 44 LYS cc_start: 0.7137 (mmtt) cc_final: 0.5804 (tmtt) REVERT: D 53 ASP cc_start: 0.7714 (p0) cc_final: 0.7298 (t0) REVERT: D 88 LEU cc_start: 0.8381 (OUTLIER) cc_final: 0.7750 (mt) REVERT: D 101 LEU cc_start: 0.7906 (OUTLIER) cc_final: 0.7508 (tt) outliers start: 11 outliers final: 7 residues processed: 97 average time/residue: 0.7162 time to fit residues: 73.9203 Evaluate side-chains 97 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 87 time to evaluate : 0.504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain D residue 102 VAL Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 0.8980 chunk 36 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 chunk 37 optimal weight: 3.9990 chunk 50 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 107 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2750 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4902 Z= 0.194 Angle : 0.581 9.542 6708 Z= 0.288 Chirality : 0.037 0.191 870 Planarity : 0.002 0.021 780 Dihedral : 9.068 50.328 1008 Min Nonbonded Distance : 2.270 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.35 % Allowed : 27.65 % Favored : 70.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.30 (0.36), residues: 594 helix: 2.69 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.71 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.034 0.002 PHE A 127 TYR 0.008 0.001 TYR B 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1188 Ramachandran restraints generated. 594 Oldfield, 0 Emsley, 594 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 85 time to evaluate : 0.520 Fit side-chains revert: symmetry clash REVERT: A 58 MET cc_start: 0.7717 (OUTLIER) cc_final: 0.7447 (mpt) REVERT: B 58 MET cc_start: 0.7514 (mtp) cc_final: 0.7195 (mtm) REVERT: B 119 ASN cc_start: 0.8307 (m-40) cc_final: 0.7976 (m-40) REVERT: C 70 GLN cc_start: 0.8463 (tp-100) cc_final: 0.8197 (tp-100) REVERT: D 44 LYS cc_start: 0.7155 (mmtt) cc_final: 0.5788 (tmtt) REVERT: D 88 LEU cc_start: 0.8406 (OUTLIER) cc_final: 0.7750 (mt) REVERT: D 101 LEU cc_start: 0.7888 (OUTLIER) cc_final: 0.7472 (tt) REVERT: F 69 GLU cc_start: 0.8190 (pt0) cc_final: 0.7986 (pt0) outliers start: 12 outliers final: 6 residues processed: 91 average time/residue: 0.7048 time to fit residues: 68.3455 Evaluate side-chains 91 residues out of total 510 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 82 time to evaluate : 0.502 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 MET Chi-restraints excluded: chain A residue 97 LEU Chi-restraints excluded: chain A residue 137 THR Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain D residue 88 LEU Chi-restraints excluded: chain D residue 101 LEU Chi-restraints excluded: chain E residue 62 SER Chi-restraints excluded: chain F residue 62 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 3.9990 chunk 41 optimal weight: 0.3980 chunk 2 optimal weight: 1.9990 chunk 34 optimal weight: 0.2980 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 63 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 133 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 63 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 = 0.4536 r_free = 0.4536 target = 0.186373 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4211 r_free = 0.4211 target = 0.155985 restraints weight = 6465.642| |-----------------------------------------------------------------------------| r_work (start): 0.4225 rms_B_bonded: 2.45 r_work: 0.4112 rms_B_bonded: 3.61 restraints_weight: 0.5000 r_work (final): 0.4112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7615 moved from start: 0.2762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4902 Z= 0.188 Angle : 0.587 10.616 6708 Z= 0.287 Chirality : 0.037 0.190 870 Planarity : 0.002 0.021 780 Dihedral : 9.032 50.625 1008 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 9.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.84 % Favored : 99.16 % Rotamer: Outliers : 2.16 % Allowed : 28.24 % Favored : 69.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.36), residues: 594 helix: 2.73 (0.23), residues: 498 sheet: None (None), residues: 0 loop : -0.69 (0.75), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 112 PHE 0.016 0.001 PHE B 74 TYR 0.007 0.001 TYR B 77 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1916.00 seconds wall clock time: 34 minutes 45.02 seconds (2085.02 seconds total)