Starting phenix.real_space_refine on Fri Sep 27 05:18:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/09_2024/7pf5_13368.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/09_2024/7pf5_13368.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/09_2024/7pf5_13368.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/09_2024/7pf5_13368.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/09_2024/7pf5_13368.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7pf5_13368/09_2024/7pf5_13368.cif" } resolution = 3.8 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= 0.008 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 2230 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 334 5.49 5 S 10 5.16 5 C 7420 2.51 5 N 2528 2.21 5 O 3178 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 24 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 13470 Number of models: 1 Model: "" Number of chains: 11 Chain: "a" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "b" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "c" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "d" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "e" Number of atoms: 798 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 798 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "f" Number of atoms: 662 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 662 Classifications: {'peptide': 83} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "g" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "h" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "J" Number of atoms: 3442 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3442 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "I" Number of atoms: 3405 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 3405 Classifications: {'DNA': 167} Link IDs: {'rna3p': 166} Chain: "u" Number of atoms: 535 Number of conformers: 1 Conformer: "" Number of residues, atoms: 75, 535 Classifications: {'peptide': 75} Link IDs: {'PTRANS': 2, 'TRANS': 72} Time building chain proxies: 7.80, per 1000 atoms: 0.58 Number of scatterers: 13470 At special positions: 0 Unit cell: (99.75, 133.35, 126, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 10 16.00 P 334 15.00 O 3178 8.00 N 2528 7.00 C 7420 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 - 3.00 Amino acid : True - 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: 3.24 Conformation dependent library (CDL) restraints added in 984.7 milliseconds 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1566 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 9 sheets defined 69.6% alpha, 2.6% beta 165 base pairs and 284 stacking pairs defined. Time for finding SS restraints: 6.71 Creating SS restraints... Processing helix chain 'a' and resid 44 through 57 Processing helix chain 'a' and resid 63 through 79 removed outlier: 3.568A pdb=" N ASP a 77 " --> pdb=" O GLU a 73 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N PHE a 78 " --> pdb=" O ILE a 74 " (cutoff:3.500A) Processing helix chain 'a' and resid 85 through 114 Processing helix chain 'a' and resid 120 through 132 removed outlier: 3.549A pdb=" N ILE a 124 " --> pdb=" O MET a 120 " (cutoff:3.500A) Processing helix chain 'b' and resid 24 through 29 Processing helix chain 'b' and resid 30 through 42 Processing helix chain 'b' and resid 49 through 77 removed outlier: 4.024A pdb=" N GLU b 53 " --> pdb=" O LEU b 49 " (cutoff:3.500A) Processing helix chain 'b' and resid 82 through 93 removed outlier: 3.566A pdb=" N GLN b 93 " --> pdb=" O ALA b 89 " (cutoff:3.500A) 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: 4.247A 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 'd' and resid 37 through 49 Processing helix chain 'd' and resid 55 through 84 Processing helix chain 'd' and resid 90 through 102 Processing helix chain 'd' and resid 103 through 123 Processing helix chain 'e' and resid 44 through 57 Processing helix chain 'e' and resid 63 through 77 removed outlier: 3.555A 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 30 through 41 Processing helix chain 'f' and resid 49 through 76 removed outlier: 3.951A pdb=" N GLU f 53 " --> pdb=" O LEU f 49 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N ASP f 68 " --> pdb=" O ASN f 64 " (cutoff:3.500A) Processing helix chain 'f' and resid 82 through 93 removed outlier: 3.572A pdb=" N GLN f 93 " --> pdb=" O ALA f 89 " (cutoff:3.500A) Processing helix chain 'g' and resid 16 through 22 Processing helix chain 'g' and resid 26 through 37 Processing helix chain 'g' and resid 45 through 73 removed outlier: 4.020A pdb=" N VAL g 49 " --> pdb=" O ALA g 45 " (cutoff:3.500A) Processing helix chain 'g' and resid 79 through 89 removed outlier: 3.507A pdb=" N ASN g 89 " --> pdb=" O LEU g 85 " (cutoff:3.500A) Processing helix chain 'g' and resid 90 through 97 Processing helix chain 'h' and resid 37 through 49 removed outlier: 3.711A pdb=" N VAL h 41 " --> pdb=" O TYR h 37 " (cutoff:3.500A) Processing helix chain 'h' and resid 55 through 84 removed outlier: 3.528A pdb=" N ASN h 84 " --> pdb=" O LEU h 80 " (cutoff:3.500A) Processing helix chain 'h' and resid 90 through 102 Processing helix chain 'h' and resid 104 through 124 removed outlier: 3.677A pdb=" N LYS h 108 " --> pdb=" O GLY h 104 " (cutoff:3.500A) Processing helix chain 'u' and resid 38 through 51 removed outlier: 3.991A pdb=" N LEU u 42 " --> pdb=" O PRO u 38 " (cutoff:3.500A) removed outlier: 4.399A pdb=" N SER u 50 " --> pdb=" O ALA u 46 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N LYS u 51 " --> pdb=" O VAL u 47 " (cutoff:3.500A) Processing helix chain 'u' and resid 58 through 69 Processing helix chain 'u' and resid 75 through 89 Processing sheet with id=AA1, first strand: chain 'a' and resid 83 through 84 removed outlier: 6.871A 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 removed outlier: 3.500A pdb=" N ILE a 119 " --> pdb=" O ARG b 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'c' and resid 42 through 43 removed outlier: 7.183A pdb=" N ARG c 42 " --> pdb=" O ILE d 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'c' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'e' and resid 83 through 84 removed outlier: 6.925A pdb=" N ARG e 83 " --> pdb=" O VAL f 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'e' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'g' and resid 42 through 43 removed outlier: 7.331A pdb=" N ARG g 42 " --> pdb=" O ILE h 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'g' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'u' and resid 56 through 57 433 hydrogen bonds defined for protein. 1287 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 423 hydrogen bonds 846 hydrogen bond angles 0 basepair planarities 165 basepair parallelities 284 stacking parallelities Total time for adding SS restraints: 6.57 Time building geometry restraints manager: 3.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2457 1.33 - 1.45: 4977 1.45 - 1.58: 6266 1.58 - 1.70: 666 1.70 - 1.82: 20 Bond restraints: 14386 Sorted by residual: bond pdb=" C3' DG J 541 " pdb=" O3' DG J 541 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.31e+00 bond pdb=" C3' DG I 335 " pdb=" O3' DG I 335 " ideal model delta sigma weight residual 1.422 1.484 -0.062 3.00e-02 1.11e+03 4.30e+00 bond pdb=" CG GLU b 53 " pdb=" CD GLU b 53 " ideal model delta sigma weight residual 1.516 1.465 0.051 2.50e-02 1.60e+03 4.10e+00 bond pdb=" CB GLU b 53 " pdb=" CG GLU b 53 " ideal model delta sigma weight residual 1.520 1.460 0.060 3.00e-02 1.11e+03 4.06e+00 bond pdb=" C3' DG I 223 " pdb=" O3' DG I 223 " ideal model delta sigma weight residual 1.422 1.478 -0.056 3.00e-02 1.11e+03 3.50e+00 ... (remaining 14381 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.17: 20149 2.17 - 4.33: 616 4.33 - 6.50: 64 6.50 - 8.67: 18 8.67 - 10.84: 6 Bond angle restraints: 20853 Sorted by residual: angle pdb=" CB ARG c 42 " pdb=" CG ARG c 42 " pdb=" CD ARG c 42 " ideal model delta sigma weight residual 111.30 121.64 -10.34 2.30e+00 1.89e-01 2.02e+01 angle pdb=" C TYR e 54 " pdb=" N GLN e 55 " pdb=" CA GLN e 55 " ideal model delta sigma weight residual 120.31 114.28 6.03 1.52e+00 4.33e-01 1.57e+01 angle pdb=" N GLN e 55 " pdb=" CA GLN e 55 " pdb=" CB GLN e 55 " ideal model delta sigma weight residual 110.28 116.01 -5.73 1.55e+00 4.16e-01 1.37e+01 angle pdb=" CB MET b 84 " pdb=" CG MET b 84 " pdb=" SD MET b 84 " ideal model delta sigma weight residual 112.70 123.54 -10.84 3.00e+00 1.11e-01 1.30e+01 angle pdb=" CB MET h 62 " pdb=" CG MET h 62 " pdb=" SD MET h 62 " ideal model delta sigma weight residual 112.70 123.36 -10.66 3.00e+00 1.11e-01 1.26e+01 ... (remaining 20848 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.82: 6119 35.82 - 71.64: 1652 71.64 - 107.45: 24 107.45 - 143.27: 1 143.27 - 179.09: 3 Dihedral angle restraints: 7799 sinusoidal: 5368 harmonic: 2431 Sorted by residual: dihedral pdb=" CA TYR e 54 " pdb=" C TYR e 54 " pdb=" N GLN e 55 " pdb=" CA GLN e 55 " ideal model delta harmonic sigma weight residual 180.00 158.38 21.62 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CA THR d 88 " pdb=" C THR d 88 " pdb=" N ILE d 89 " pdb=" CA ILE d 89 " ideal model delta harmonic sigma weight residual 180.00 160.16 19.84 0 5.00e+00 4.00e-02 1.57e+01 dihedral pdb=" C4' DG I 335 " pdb=" C3' DG I 335 " pdb=" O3' DG I 335 " pdb=" P DT I 336 " ideal model delta sinusoidal sigma weight residual -140.00 39.09 -179.09 1 3.50e+01 8.16e-04 1.57e+01 ... (remaining 7796 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 1769 0.048 - 0.096: 476 0.096 - 0.144: 103 0.144 - 0.192: 20 0.192 - 0.239: 8 Chirality restraints: 2376 Sorted by residual: chirality pdb=" CA GLN e 55 " pdb=" N GLN e 55 " pdb=" C GLN e 55 " pdb=" CB GLN e 55 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.43e+00 chirality pdb=" CB ILE d 89 " pdb=" CA ILE d 89 " pdb=" CG1 ILE d 89 " pdb=" CG2 ILE d 89 " both_signs ideal model delta sigma weight residual False 2.64 2.42 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU a 92 " pdb=" CB LEU a 92 " pdb=" CD1 LEU a 92 " pdb=" CD2 LEU a 92 " both_signs ideal model delta sigma weight residual False -2.59 -2.81 0.22 2.00e-01 2.50e+01 1.25e+00 ... (remaining 2373 not shown) Planarity restraints: 1478 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE e 51 " 0.018 2.00e-02 2.50e+03 3.52e-02 1.24e+01 pdb=" C ILE e 51 " -0.061 2.00e-02 2.50e+03 pdb=" O ILE e 51 " 0.023 2.00e-02 2.50e+03 pdb=" N ARG e 52 " 0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL f 70 " 0.014 2.00e-02 2.50e+03 2.88e-02 8.31e+00 pdb=" C VAL f 70 " -0.050 2.00e-02 2.50e+03 pdb=" O VAL f 70 " 0.019 2.00e-02 2.50e+03 pdb=" N THR f 71 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG d 99 " 0.206 9.50e-02 1.11e+02 9.27e-02 6.37e+00 pdb=" NE ARG d 99 " -0.019 2.00e-02 2.50e+03 pdb=" CZ ARG d 99 " 0.016 2.00e-02 2.50e+03 pdb=" NH1 ARG d 99 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG d 99 " 0.001 2.00e-02 2.50e+03 ... (remaining 1475 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2832 2.79 - 3.32: 12441 3.32 - 3.85: 28918 3.85 - 4.37: 31999 4.37 - 4.90: 44664 Nonbonded interactions: 120854 Sorted by model distance: nonbonded pdb=" O TYR c 39 " pdb=" OG SER d 78 " model vdw 2.264 3.040 nonbonded pdb=" NH2 ARG c 81 " pdb=" O GLN e 55 " model vdw 2.273 3.120 nonbonded pdb=" NH1 ARG g 29 " pdb=" OE2 GLU h 35 " model vdw 2.295 3.120 nonbonded pdb=" ND2 ASN a 108 " pdb=" O GLY b 42 " model vdw 2.296 3.120 nonbonded pdb=" O THR g 16 " pdb=" OG SER g 19 " model vdw 2.296 3.040 ... (remaining 120849 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = chain 'b' selection = chain 'f' } ncs_group { reference = chain 'c' selection = chain 'g' } ncs_group { reference = chain 'd' selection = chain 'h' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.530 Check model and map are aligned: 0.100 Set scattering table: 0.130 Process input model: 37.540 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.071 14386 Z= 0.352 Angle : 0.889 10.836 20853 Z= 0.497 Chirality : 0.048 0.239 2376 Planarity : 0.007 0.093 1478 Dihedral : 28.940 179.090 6233 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.82 % Favored : 98.18 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -0.59 (0.26), residues: 825 helix: -0.07 (0.19), residues: 573 sheet: -0.81 (1.73), residues: 10 loop : -0.85 (0.34), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.009 0.002 HIS f 75 PHE 0.043 0.002 PHE e 104 TYR 0.034 0.004 TYR a 54 ARG 0.018 0.001 ARG d 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 150 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 150 time to evaluate : 1.043 Fit side-chains revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9120 (m-80) cc_final: 0.8695 (m-80) REVERT: a 90 MET cc_start: 0.8857 (mpp) cc_final: 0.8634 (mpp) REVERT: b 63 GLU cc_start: 0.9360 (mt-10) cc_final: 0.9110 (mt-10) REVERT: b 70 VAL cc_start: 0.9567 (t) cc_final: 0.9284 (t) REVERT: b 85 ASP cc_start: 0.7900 (m-30) cc_final: 0.7678 (m-30) REVERT: c 30 VAL cc_start: 0.8230 (t) cc_final: 0.8020 (t) REVERT: c 36 LYS cc_start: 0.8885 (mmpt) cc_final: 0.8596 (mmmt) REVERT: c 61 GLU cc_start: 0.8679 (mt-10) cc_final: 0.8120 (mt-10) REVERT: d 65 PHE cc_start: 0.8827 (t80) cc_final: 0.8617 (t80) REVERT: f 74 GLU cc_start: 0.8709 (pm20) cc_final: 0.8438 (pm20) REVERT: g 61 GLU cc_start: 0.8820 (tm-30) cc_final: 0.8497 (tm-30) REVERT: g 62 ILE cc_start: 0.9528 (pt) cc_final: 0.9196 (pt) REVERT: g 95 LYS cc_start: 0.8892 (tptt) cc_final: 0.8211 (mmmm) REVERT: h 33 ARG cc_start: 0.6629 (mtp-110) cc_final: 0.6114 (mtt-85) REVERT: h 51 ASP cc_start: 0.8619 (p0) cc_final: 0.8408 (p0) REVERT: h 105 GLU cc_start: 0.8526 (tp30) cc_final: 0.8152 (tp30) REVERT: h 108 LYS cc_start: 0.9413 (ptpt) cc_final: 0.9175 (ptpp) outliers start: 0 outliers final: 0 residues processed: 150 average time/residue: 0.2700 time to fit residues: 57.3297 Evaluate side-chains 103 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 103 time to evaluate : 1.021 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 7.9990 chunk 84 optimal weight: 7.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 87 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.2980 chunk 64 optimal weight: 2.9990 chunk 100 optimal weight: 5.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** u 94 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.1787 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 14386 Z= 0.199 Angle : 0.624 9.466 20853 Z= 0.365 Chirality : 0.035 0.159 2376 Planarity : 0.005 0.058 1478 Dihedral : 31.623 179.994 4581 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer: Outliers : 0.72 % Allowed : 9.67 % Favored : 89.61 % 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: 0.62 (0.27), residues: 825 helix: 0.88 (0.20), residues: 586 sheet: -0.09 (1.97), residues: 10 loop : -0.58 (0.36), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS b 75 PHE 0.010 0.001 PHE e 104 TYR 0.023 0.002 TYR c 57 ARG 0.005 0.001 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 129 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9136 (m-80) cc_final: 0.8552 (m-80) REVERT: a 97 GLU cc_start: 0.8252 (tt0) cc_final: 0.7882 (tt0) REVERT: b 63 GLU cc_start: 0.9398 (mt-10) cc_final: 0.8653 (mp0) REVERT: b 85 ASP cc_start: 0.7815 (m-30) cc_final: 0.7582 (m-30) REVERT: c 36 LYS cc_start: 0.8836 (mmpt) cc_final: 0.8463 (mmmt) REVERT: d 105 GLU cc_start: 0.8411 (pm20) cc_final: 0.8161 (pm20) REVERT: f 63 GLU cc_start: 0.8921 (mm-30) cc_final: 0.8444 (mm-30) REVERT: f 84 MET cc_start: 0.7670 (tpp) cc_final: 0.7449 (tpp) REVERT: f 90 LEU cc_start: 0.8752 (mm) cc_final: 0.8545 (mm) REVERT: g 61 GLU cc_start: 0.8889 (tm-30) cc_final: 0.8542 (tm-30) REVERT: g 62 ILE cc_start: 0.9508 (pt) cc_final: 0.9132 (pt) REVERT: g 95 LYS cc_start: 0.8809 (tptt) cc_final: 0.8161 (mmmm) REVERT: h 33 ARG cc_start: 0.6369 (mtp-110) cc_final: 0.5613 (mtt-85) REVERT: h 51 ASP cc_start: 0.8671 (p0) cc_final: 0.8332 (p0) REVERT: h 105 GLU cc_start: 0.8606 (tp30) cc_final: 0.8214 (tp30) outliers start: 5 outliers final: 4 residues processed: 132 average time/residue: 0.2698 time to fit residues: 50.9676 Evaluate side-chains 108 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 104 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain f residue 22 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 3.9990 chunk 83 optimal weight: 7.9990 chunk 68 optimal weight: 2.9990 chunk 27 optimal weight: 8.9990 chunk 100 optimal weight: 5.9990 chunk 109 optimal weight: 8.9990 chunk 89 optimal weight: 7.9990 chunk 34 optimal weight: 0.9990 chunk 81 optimal weight: 8.9990 chunk 99 optimal weight: 5.9990 overall best weight: 2.9188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** a 108 ASN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.2789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 14386 Z= 0.320 Angle : 0.658 9.809 20853 Z= 0.385 Chirality : 0.037 0.145 2376 Planarity : 0.005 0.056 1478 Dihedral : 31.757 174.609 4581 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 2.02 % Allowed : 11.54 % Favored : 86.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.28), residues: 825 helix: 1.15 (0.21), residues: 590 sheet: -0.57 (1.91), residues: 10 loop : -0.59 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS f 75 PHE 0.012 0.002 PHE g 25 TYR 0.027 0.003 TYR h 83 ARG 0.007 0.001 ARG a 131 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 111 time to evaluate : 1.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9115 (m-80) cc_final: 0.8549 (m-80) REVERT: a 97 GLU cc_start: 0.8414 (tt0) cc_final: 0.8057 (tt0) REVERT: a 108 ASN cc_start: 0.9318 (OUTLIER) cc_final: 0.9090 (t0) REVERT: b 85 ASP cc_start: 0.7837 (m-30) cc_final: 0.7607 (m-30) REVERT: c 36 LYS cc_start: 0.8951 (mmpt) cc_final: 0.8567 (mmmt) REVERT: e 105 GLU cc_start: 0.8830 (mm-30) cc_final: 0.8618 (mm-30) REVERT: f 63 GLU cc_start: 0.9052 (mm-30) cc_final: 0.8718 (mm-30) REVERT: g 61 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8566 (tm-30) REVERT: g 62 ILE cc_start: 0.9537 (pt) cc_final: 0.9210 (pt) REVERT: h 51 ASP cc_start: 0.8603 (p0) cc_final: 0.8385 (p0) REVERT: h 105 GLU cc_start: 0.8717 (tp30) cc_final: 0.8375 (tp30) outliers start: 14 outliers final: 11 residues processed: 120 average time/residue: 0.2687 time to fit residues: 45.9475 Evaluate side-chains 107 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 95 time to evaluate : 1.025 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain a residue 108 ASN Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 54 VAL Chi-restraints excluded: chain g residue 76 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 7.9990 chunk 52 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 6.9990 chunk 67 optimal weight: 0.9990 chunk 101 optimal weight: 6.9990 chunk 107 optimal weight: 10.0000 chunk 96 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 89 optimal weight: 7.9990 chunk 60 optimal weight: 2.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** a 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 14386 Z= 0.254 Angle : 0.621 10.853 20853 Z= 0.362 Chirality : 0.035 0.175 2376 Planarity : 0.004 0.058 1478 Dihedral : 31.639 176.278 4581 Min Nonbonded Distance : 2.478 Molprobity Statistics. All-atom Clashscore : 14.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.55 % Favored : 97.45 % Rotamer: Outliers : 1.88 % Allowed : 13.85 % Favored : 84.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.28), residues: 825 helix: 1.31 (0.21), residues: 588 sheet: -0.85 (1.84), residues: 10 loop : -0.63 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS f 75 PHE 0.007 0.001 PHE e 104 TYR 0.024 0.002 TYR b 88 ARG 0.004 0.000 ARG f 95 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 117 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9061 (m-80) cc_final: 0.8482 (m-80) REVERT: a 90 MET cc_start: 0.8848 (mpp) cc_final: 0.8504 (mmm) REVERT: a 97 GLU cc_start: 0.8370 (tt0) cc_final: 0.8140 (tt0) REVERT: c 36 LYS cc_start: 0.8946 (mmpt) cc_final: 0.8562 (mmmt) REVERT: e 97 GLU cc_start: 0.8239 (mt-10) cc_final: 0.8038 (mt-10) REVERT: e 105 GLU cc_start: 0.8822 (mm-30) cc_final: 0.8563 (mm-30) REVERT: f 63 GLU cc_start: 0.8900 (mm-30) cc_final: 0.8575 (mm-30) REVERT: g 61 GLU cc_start: 0.8936 (tm-30) cc_final: 0.8554 (tm-30) REVERT: g 62 ILE cc_start: 0.9562 (pt) cc_final: 0.9238 (pt) REVERT: h 51 ASP cc_start: 0.8663 (p0) cc_final: 0.8404 (p0) REVERT: h 105 GLU cc_start: 0.8722 (tp30) cc_final: 0.8454 (tp30) REVERT: h 108 LYS cc_start: 0.9262 (ptpt) cc_final: 0.8995 (pttm) outliers start: 13 outliers final: 8 residues processed: 124 average time/residue: 0.2597 time to fit residues: 46.6539 Evaluate side-chains 111 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 103 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 76 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 chunk 44 optimal weight: 0.6980 chunk 91 optimal weight: 6.9990 chunk 74 optimal weight: 8.9990 chunk 0 optimal weight: 10.0000 chunk 54 optimal weight: 8.9990 chunk 96 optimal weight: 6.9990 chunk 27 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 overall best weight: 3.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** a 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.3960 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.065 14386 Z= 0.346 Angle : 0.668 11.306 20853 Z= 0.387 Chirality : 0.037 0.195 2376 Planarity : 0.005 0.057 1478 Dihedral : 31.871 176.102 4581 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 2.16 % Allowed : 15.87 % Favored : 81.96 % 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: 0.92 (0.28), residues: 825 helix: 1.17 (0.20), residues: 588 sheet: -0.89 (1.92), residues: 10 loop : -0.67 (0.36), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS f 75 PHE 0.011 0.002 PHE a 104 TYR 0.017 0.002 TYR c 39 ARG 0.006 0.001 ARG f 95 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.124 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9098 (m-80) cc_final: 0.8572 (m-80) REVERT: a 97 GLU cc_start: 0.8248 (tt0) cc_final: 0.8024 (tt0) REVERT: b 74 GLU cc_start: 0.9044 (pt0) cc_final: 0.8813 (pm20) REVERT: c 36 LYS cc_start: 0.8935 (mmpt) cc_final: 0.8536 (mmmt) REVERT: c 61 GLU cc_start: 0.8542 (tm-30) cc_final: 0.8100 (tm-30) REVERT: e 97 GLU cc_start: 0.8212 (mt-10) cc_final: 0.7957 (mt-10) REVERT: e 105 GLU cc_start: 0.8798 (mm-30) cc_final: 0.8498 (mm-30) REVERT: f 63 GLU cc_start: 0.8926 (mm-30) cc_final: 0.8625 (mm-30) REVERT: g 61 GLU cc_start: 0.8958 (tm-30) cc_final: 0.8559 (tm-30) REVERT: g 62 ILE cc_start: 0.9552 (pt) cc_final: 0.9290 (pt) REVERT: h 105 GLU cc_start: 0.8754 (tp30) cc_final: 0.8523 (tp30) REVERT: h 108 LYS cc_start: 0.9240 (ptpt) cc_final: 0.8966 (pttm) outliers start: 15 outliers final: 14 residues processed: 114 average time/residue: 0.2721 time to fit residues: 44.4140 Evaluate side-chains 112 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 98 time to evaluate : 0.968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 102 ILE Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 39 VAL Chi-restraints excluded: chain d residue 52 THR Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 22 LEU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 76 THR Chi-restraints excluded: chain g residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 7.9990 chunk 26 optimal weight: 6.9990 chunk 107 optimal weight: 0.9980 chunk 89 optimal weight: 7.9990 chunk 49 optimal weight: 0.7980 chunk 8 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: a 76 GLN ** b 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** f 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8042 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 14386 Z= 0.201 Angle : 0.619 11.500 20853 Z= 0.358 Chirality : 0.034 0.171 2376 Planarity : 0.004 0.057 1478 Dihedral : 31.546 176.683 4581 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 14.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.42 % Favored : 97.58 % Rotamer: Outliers : 1.30 % Allowed : 18.04 % Favored : 80.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.11 (0.28), residues: 825 helix: 1.32 (0.21), residues: 590 sheet: -1.16 (1.74), residues: 10 loop : -0.61 (0.37), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS d 49 PHE 0.006 0.001 PHE e 104 TYR 0.013 0.002 TYR c 57 ARG 0.009 0.000 ARG g 20 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 127 time to evaluate : 1.037 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 54 TYR cc_start: 0.9007 (m-80) cc_final: 0.8531 (m-80) REVERT: a 97 GLU cc_start: 0.8284 (tt0) cc_final: 0.7993 (tt0) REVERT: c 36 LYS cc_start: 0.8843 (mmpt) cc_final: 0.8471 (mmmt) REVERT: d 76 GLU cc_start: 0.8270 (tp30) cc_final: 0.7391 (tp30) REVERT: d 79 ARG cc_start: 0.9065 (ptp-110) cc_final: 0.8721 (mtm110) REVERT: e 97 GLU cc_start: 0.8185 (mt-10) cc_final: 0.7869 (mt-10) REVERT: e 105 GLU cc_start: 0.8791 (mm-30) cc_final: 0.8513 (mm-30) REVERT: f 63 GLU cc_start: 0.8853 (mm-30) cc_final: 0.8569 (mm-30) REVERT: g 61 GLU cc_start: 0.8896 (tm-30) cc_final: 0.8502 (tm-30) REVERT: g 62 ILE cc_start: 0.9566 (pt) cc_final: 0.9237 (pt) REVERT: h 51 ASP cc_start: 0.8663 (p0) cc_final: 0.8430 (p0) REVERT: h 108 LYS cc_start: 0.9270 (ptpt) cc_final: 0.8963 (pttm) outliers start: 9 outliers final: 9 residues processed: 133 average time/residue: 0.2638 time to fit residues: 50.4718 Evaluate side-chains 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 106 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain e residue 120 MET Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 107 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 8.9990 chunk 60 optimal weight: 0.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 7.9990 chunk 106 optimal weight: 30.0000 chunk 66 optimal weight: 0.9990 chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 42 optimal weight: 0.9980 chunk 63 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.4247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14386 Z= 0.217 Angle : 0.621 11.342 20853 Z= 0.359 Chirality : 0.034 0.152 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.505 176.564 4581 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 1.44 % Allowed : 19.62 % Favored : 78.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.08 (0.28), residues: 825 helix: 1.28 (0.21), residues: 588 sheet: -1.20 (1.69), residues: 10 loop : -0.53 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS h 109 PHE 0.008 0.001 PHE e 67 TYR 0.035 0.002 TYR h 83 ARG 0.002 0.000 ARG c 42 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 114 time to evaluate : 1.082 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 54 TYR cc_start: 0.9022 (m-80) cc_final: 0.8541 (m-80) REVERT: a 97 GLU cc_start: 0.8343 (tt0) cc_final: 0.8044 (tt0) REVERT: b 59 LYS cc_start: 0.9461 (tptp) cc_final: 0.8883 (tptp) REVERT: b 63 GLU cc_start: 0.9291 (mt-10) cc_final: 0.8715 (mp0) REVERT: c 36 LYS cc_start: 0.8858 (mmpt) cc_final: 0.8472 (mmmt) REVERT: e 97 GLU cc_start: 0.8280 (mt-10) cc_final: 0.7916 (mt-10) REVERT: e 105 GLU cc_start: 0.8816 (mm-30) cc_final: 0.8571 (mm-30) REVERT: g 61 GLU cc_start: 0.8917 (tm-30) cc_final: 0.8474 (tm-30) REVERT: g 62 ILE cc_start: 0.9563 (pt) cc_final: 0.9246 (pt) REVERT: g 90 ASP cc_start: 0.7819 (t70) cc_final: 0.7046 (p0) REVERT: h 51 ASP cc_start: 0.8687 (p0) cc_final: 0.8416 (p0) REVERT: h 85 LYS cc_start: 0.9117 (mppt) cc_final: 0.8905 (mmtm) REVERT: h 108 LYS cc_start: 0.9313 (ptpt) cc_final: 0.8979 (ptpp) outliers start: 10 outliers final: 7 residues processed: 121 average time/residue: 0.2598 time to fit residues: 45.5896 Evaluate side-chains 118 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 111 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 74 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 6.9990 chunk 72 optimal weight: 10.0000 chunk 52 optimal weight: 0.6980 chunk 9 optimal weight: 6.9990 chunk 84 optimal weight: 7.9990 chunk 97 optimal weight: 7.9990 chunk 102 optimal weight: 7.9990 chunk 93 optimal weight: 6.9990 chunk 99 optimal weight: 7.9990 overall best weight: 3.2784 ------------------------------------------------------------------------------- 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** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.4719 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 14386 Z= 0.338 Angle : 0.673 11.956 20853 Z= 0.386 Chirality : 0.037 0.172 2376 Planarity : 0.005 0.055 1478 Dihedral : 31.894 176.824 4581 Min Nonbonded Distance : 2.414 Molprobity Statistics. All-atom Clashscore : 18.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.59 % Allowed : 19.62 % Favored : 78.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.28), residues: 825 helix: 1.04 (0.21), residues: 588 sheet: -1.07 (1.79), residues: 10 loop : -0.66 (0.37), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS b 75 PHE 0.009 0.001 PHE a 104 TYR 0.050 0.002 TYR h 83 ARG 0.005 0.001 ARG f 95 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 102 time to evaluate : 1.008 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9122 (m-80) cc_final: 0.8574 (m-80) REVERT: a 97 GLU cc_start: 0.8408 (tt0) cc_final: 0.8141 (tt0) REVERT: b 59 LYS cc_start: 0.9467 (tptp) cc_final: 0.8942 (tptp) REVERT: b 63 GLU cc_start: 0.9298 (mt-10) cc_final: 0.8751 (mp0) REVERT: c 36 LYS cc_start: 0.8822 (mmpt) cc_final: 0.8459 (mmmt) REVERT: c 41 GLU cc_start: 0.8343 (pm20) cc_final: 0.8100 (pm20) REVERT: e 97 GLU cc_start: 0.8291 (mt-10) cc_final: 0.7893 (mt-10) REVERT: g 61 GLU cc_start: 0.8970 (tm-30) cc_final: 0.8561 (tm-30) REVERT: g 62 ILE cc_start: 0.9585 (pt) cc_final: 0.9309 (pt) REVERT: h 85 LYS cc_start: 0.9216 (mppt) cc_final: 0.9000 (mmtm) REVERT: h 108 LYS cc_start: 0.9279 (ptpt) cc_final: 0.8932 (ptpp) outliers start: 11 outliers final: 9 residues processed: 110 average time/residue: 0.2541 time to fit residues: 40.3467 Evaluate side-chains 107 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 78 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 8.9990 chunk 99 optimal weight: 6.9990 chunk 65 optimal weight: 6.9990 chunk 105 optimal weight: 30.0000 chunk 64 optimal weight: 0.8980 overall best weight: 2.9786 ------------------------------------------------------------------------------- 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** ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8141 moved from start: 0.5079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 14386 Z= 0.312 Angle : 0.671 11.840 20853 Z= 0.385 Chirality : 0.036 0.169 2376 Planarity : 0.004 0.056 1478 Dihedral : 31.886 177.011 4581 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer: Outliers : 1.88 % Allowed : 20.35 % Favored : 77.78 % 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: 0.76 (0.28), residues: 825 helix: 1.02 (0.21), residues: 590 sheet: -1.32 (1.76), residues: 10 loop : -0.64 (0.38), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS c 82 PHE 0.009 0.001 PHE g 25 TYR 0.052 0.002 TYR h 83 ARG 0.004 0.001 ARG c 81 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 108 time to evaluate : 1.068 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.9061 (m-80) cc_final: 0.8505 (m-80) REVERT: a 97 GLU cc_start: 0.8367 (tt0) cc_final: 0.8101 (tt0) REVERT: b 59 LYS cc_start: 0.9489 (tptp) cc_final: 0.8969 (tptp) REVERT: b 63 GLU cc_start: 0.9293 (mt-10) cc_final: 0.8706 (mp0) REVERT: c 36 LYS cc_start: 0.8768 (mmpt) cc_final: 0.8369 (mmmt) REVERT: c 41 GLU cc_start: 0.8346 (pm20) cc_final: 0.8099 (pm20) REVERT: e 97 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7873 (mt-10) REVERT: f 63 GLU cc_start: 0.9058 (mm-30) cc_final: 0.8787 (mp0) REVERT: f 92 ARG cc_start: 0.8839 (OUTLIER) cc_final: 0.7850 (ttp-110) REVERT: g 61 GLU cc_start: 0.8963 (tm-30) cc_final: 0.8564 (tm-30) REVERT: g 62 ILE cc_start: 0.9577 (pt) cc_final: 0.9295 (pt) REVERT: h 108 LYS cc_start: 0.9287 (ptpt) cc_final: 0.8921 (ptpp) REVERT: h 109 HIS cc_start: 0.8528 (m170) cc_final: 0.7969 (m90) outliers start: 13 outliers final: 11 residues processed: 119 average time/residue: 0.2647 time to fit residues: 45.2792 Evaluate side-chains 115 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 1.019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 46 VAL Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 79 ILE Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 107 VAL Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 38 SER Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 92 ARG Chi-restraints excluded: chain g residue 16 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 1.9990 chunk 73 optimal weight: 7.9990 chunk 110 optimal weight: 7.9990 chunk 101 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 chunk 9 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 53 optimal weight: 0.9980 chunk 69 optimal weight: 0.7980 chunk 93 optimal weight: 6.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: b 25 ASN ** e 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8051 moved from start: 0.5178 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14386 Z= 0.211 Angle : 0.652 11.776 20853 Z= 0.371 Chirality : 0.035 0.158 2376 Planarity : 0.004 0.057 1478 Dihedral : 31.531 177.007 4581 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 14.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 1.15 % Allowed : 21.65 % Favored : 77.20 % 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: 0.89 (0.28), residues: 825 helix: 1.11 (0.21), residues: 590 sheet: -1.62 (1.62), residues: 10 loop : -0.51 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS d 49 PHE 0.007 0.001 PHE c 25 TYR 0.044 0.002 TYR h 83 ARG 0.004 0.000 ARG h 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1650 Ramachandran restraints generated. 825 Oldfield, 0 Emsley, 825 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 124 time to evaluate : 1.064 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: a 54 TYR cc_start: 0.8970 (m-80) cc_final: 0.8488 (m-80) REVERT: a 79 LYS cc_start: 0.9260 (tttm) cc_final: 0.9047 (tttm) REVERT: a 97 GLU cc_start: 0.8289 (tt0) cc_final: 0.8039 (tt0) REVERT: b 59 LYS cc_start: 0.9388 (tptp) cc_final: 0.9124 (tptp) REVERT: b 63 GLU cc_start: 0.9188 (mt-10) cc_final: 0.8651 (mt-10) REVERT: c 36 LYS cc_start: 0.8831 (mmpt) cc_final: 0.8467 (mmmt) REVERT: d 51 ASP cc_start: 0.8935 (p0) cc_final: 0.8693 (t0) REVERT: d 99 ARG cc_start: 0.8809 (mtp85) cc_final: 0.8581 (mtt-85) REVERT: e 97 GLU cc_start: 0.8176 (mt-10) cc_final: 0.7863 (mt-10) REVERT: e 123 ASP cc_start: 0.8017 (m-30) cc_final: 0.7767 (m-30) REVERT: f 63 GLU cc_start: 0.8936 (mm-30) cc_final: 0.8717 (mp0) REVERT: f 92 ARG cc_start: 0.8800 (OUTLIER) cc_final: 0.8485 (tmm-80) REVERT: g 61 GLU cc_start: 0.8920 (tm-30) cc_final: 0.8522 (tm-30) REVERT: g 62 ILE cc_start: 0.9574 (pt) cc_final: 0.9259 (pt) REVERT: h 51 ASP cc_start: 0.8590 (p0) cc_final: 0.8307 (p0) REVERT: h 108 LYS cc_start: 0.9291 (ptpt) cc_final: 0.8919 (ptpp) REVERT: h 109 HIS cc_start: 0.8472 (m170) cc_final: 0.7908 (m90) outliers start: 8 outliers final: 6 residues processed: 129 average time/residue: 0.2680 time to fit residues: 50.1197 Evaluate side-chains 123 residues out of total 693 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 116 time to evaluate : 1.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain a residue 77 ASP Chi-restraints excluded: chain c residue 94 ASN Chi-restraints excluded: chain c residue 114 VAL Chi-restraints excluded: chain d residue 113 GLU Chi-restraints excluded: chain e residue 117 VAL Chi-restraints excluded: chain f residue 74 GLU Chi-restraints excluded: chain f residue 92 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 10.0000 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 10.0000 chunk 36 optimal weight: 10.0000 chunk 90 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 77 optimal weight: 6.9990 chunk 5 optimal weight: 0.9990 chunk 63 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** e 113 HIS ** 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 = 0.3381 r_free = 0.3381 target = 0.039392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3025 r_free = 0.3025 target = 0.031918 restraints weight = 131537.756| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.032765 restraints weight = 74223.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.033313 restraints weight = 51197.125| |-----------------------------------------------------------------------------| r_work (final): 0.3065 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.5320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14386 Z= 0.227 Angle : 0.641 13.342 20853 Z= 0.366 Chirality : 0.035 0.185 2376 Planarity : 0.004 0.061 1478 Dihedral : 31.522 177.114 4581 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer: Outliers : 0.87 % Allowed : 21.36 % Favored : 77.78 % 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: 0.82 (0.28), residues: 825 helix: 1.01 (0.21), residues: 590 sheet: -1.58 (1.63), residues: 10 loop : -0.40 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.003 0.001 HIS h 82 PHE 0.008 0.001 PHE e 104 TYR 0.030 0.002 TYR h 83 ARG 0.004 0.000 ARG d 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1985.94 seconds wall clock time: 36 minutes 50.82 seconds (2210.82 seconds total)