Starting phenix.real_space_refine on Thu Sep 26 05:19:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/09_2024/7y00_33536.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/09_2024/7y00_33536.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/09_2024/7y00_33536.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/09_2024/7y00_33536.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/09_2024/7y00_33536.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y00_33536/09_2024/7y00_33536.cif" } resolution = 3.96 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 310 5.49 5 S 14 5.16 5 C 6823 2.51 5 N 2339 2.21 5 O 2925 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 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: 12411 Number of models: 1 Model: "" Number of chains: 10 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 844 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 810 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 810 Classifications: {'peptide': 98} Link IDs: {'PTRANS': 4, 'TRANS': 93} Chain: "F" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "G" Number of atoms: 819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 819 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 5, 'TRANS': 100} Chain: "H" Number of atoms: 746 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 746 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 3166 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3166 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Chain: "J" Number of atoms: 3189 Number of conformers: 1 Conformer: "" Number of residues, atoms: 155, 3189 Classifications: {'DNA': 155} Link IDs: {'rna3p': 154} Time building chain proxies: 7.27, per 1000 atoms: 0.59 Number of scatterers: 12411 At special positions: 0 Unit cell: (116.6, 147.34, 113.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 310 15.00 O 2925 8.00 N 2339 7.00 C 6823 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 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: 3.00 Conformation dependent library (CDL) restraints added in 888.4 milliseconds 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1420 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 73.5% alpha, 3.1% beta 153 base pairs and 247 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 77 removed outlier: 4.096A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.292A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.117A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.995A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 121 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.537A pdb=" N SER E 57 " --> pdb=" O ARG E 53 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.553A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.757A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.880A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.268A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 removed outlier: 3.523A pdb=" N ILE H 91 " --> pdb=" O THR H 87 " (cutoff:3.500A) Processing helix chain 'H' and resid 100 through 122 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.999A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.082A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 removed outlier: 3.757A pdb=" N ILE C 78 " --> pdb=" O GLY D 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 removed outlier: 3.501A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.761A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.342A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 removed outlier: 3.547A pdb=" N ILE G 78 " --> pdb=" O GLY H 50 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 415 hydrogen bonds defined for protein. 1218 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 395 hydrogen bonds 786 hydrogen bond angles 0 basepair planarities 153 basepair parallelities 247 stacking parallelities Total time for adding SS restraints: 4.15 Time building geometry restraints manager: 3.51 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2627 1.34 - 1.46: 4279 1.46 - 1.57: 5716 1.57 - 1.69: 618 1.69 - 1.81: 24 Bond restraints: 13264 Sorted by residual: bond pdb=" C1' DG J 31 " pdb=" N9 DG J 31 " ideal model delta sigma weight residual 1.460 1.391 0.069 2.00e-02 2.50e+03 1.20e+01 bond pdb=" N ILE C 87 " pdb=" CA ILE C 87 " ideal model delta sigma weight residual 1.460 1.492 -0.032 1.19e-02 7.06e+03 7.08e+00 bond pdb=" N ILE H 66 " pdb=" CA ILE H 66 " ideal model delta sigma weight residual 1.461 1.492 -0.031 1.17e-02 7.31e+03 7.02e+00 bond pdb=" N ILE G 87 " pdb=" CA ILE G 87 " ideal model delta sigma weight residual 1.460 1.491 -0.032 1.21e-02 6.83e+03 6.79e+00 bond pdb=" N ILE D 66 " pdb=" CA ILE D 66 " ideal model delta sigma weight residual 1.461 1.491 -0.029 1.17e-02 7.31e+03 6.31e+00 ... (remaining 13259 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.73: 18571 1.73 - 3.46: 609 3.46 - 5.19: 40 5.19 - 6.92: 15 6.92 - 8.65: 3 Bond angle restraints: 19238 Sorted by residual: angle pdb=" N GLN E 76 " pdb=" CA GLN E 76 " pdb=" CB GLN E 76 " ideal model delta sigma weight residual 110.32 117.12 -6.80 1.70e+00 3.46e-01 1.60e+01 angle pdb=" C ALA E 75 " pdb=" N GLN E 76 " pdb=" CA GLN E 76 " ideal model delta sigma weight residual 120.60 115.14 5.46 1.60e+00 3.91e-01 1.16e+01 angle pdb=" N ILE D 66 " pdb=" CA ILE D 66 " pdb=" C ILE D 66 " ideal model delta sigma weight residual 110.42 107.17 3.25 9.60e-01 1.09e+00 1.14e+01 angle pdb=" N ILE H 66 " pdb=" CA ILE H 66 " pdb=" C ILE H 66 " ideal model delta sigma weight residual 110.42 107.39 3.03 9.60e-01 1.09e+00 9.97e+00 angle pdb=" C GLU G 56 " pdb=" CA GLU G 56 " pdb=" CB GLU G 56 " ideal model delta sigma weight residual 110.88 105.92 4.96 1.57e+00 4.06e-01 9.96e+00 ... (remaining 19233 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 4655 17.78 - 35.56: 1125 35.56 - 53.34: 1042 53.34 - 71.13: 324 71.13 - 88.91: 19 Dihedral angle restraints: 7165 sinusoidal: 4961 harmonic: 2204 Sorted by residual: dihedral pdb=" CA PRO D 100 " pdb=" C PRO D 100 " pdb=" N GLY D 101 " pdb=" CA GLY D 101 " ideal model delta harmonic sigma weight residual -180.00 -163.74 -16.26 0 5.00e+00 4.00e-02 1.06e+01 dihedral pdb=" CA ILE G 87 " pdb=" CB ILE G 87 " pdb=" CG1 ILE G 87 " pdb=" CD1 ILE G 87 " ideal model delta sinusoidal sigma weight residual 180.00 122.74 57.26 3 1.50e+01 4.44e-03 9.43e+00 dihedral pdb=" CG ARG E 128 " pdb=" CD ARG E 128 " pdb=" NE ARG E 128 " pdb=" CZ ARG E 128 " ideal model delta sinusoidal sigma weight residual -180.00 -138.72 -41.28 2 1.50e+01 4.44e-03 9.29e+00 ... (remaining 7162 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.046: 1839 0.046 - 0.091: 267 0.091 - 0.137: 65 0.137 - 0.182: 8 0.182 - 0.228: 5 Chirality restraints: 2184 Sorted by residual: chirality pdb=" CA GLU C 61 " pdb=" N GLU C 61 " pdb=" C GLU C 61 " pdb=" CB GLU C 61 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.30e+00 chirality pdb=" CB THR D 112 " pdb=" CA THR D 112 " pdb=" OG1 THR D 112 " pdb=" CG2 THR D 112 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 8.77e-01 chirality pdb=" CB VAL G 54 " pdb=" CA VAL G 54 " pdb=" CG1 VAL G 54 " pdb=" CG2 VAL G 54 " both_signs ideal model delta sigma weight residual False -2.63 -2.44 -0.19 2.00e-01 2.50e+01 8.69e-01 ... (remaining 2181 not shown) Planarity restraints: 1361 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA G 52 " -0.022 2.00e-02 2.50e+03 4.45e-02 1.98e+01 pdb=" C ALA G 52 " 0.077 2.00e-02 2.50e+03 pdb=" O ALA G 52 " -0.029 2.00e-02 2.50e+03 pdb=" N ALA G 53 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" C LYS F 59 " 0.053 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.020 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER E 87 " 0.008 2.00e-02 2.50e+03 1.64e-02 2.70e+00 pdb=" C SER E 87 " -0.028 2.00e-02 2.50e+03 pdb=" O SER E 87 " 0.011 2.00e-02 2.50e+03 pdb=" N ALA E 88 " 0.010 2.00e-02 2.50e+03 ... (remaining 1358 not shown) Histogram of nonbonded interaction distances: 1.72 - 2.35: 27 2.35 - 2.99: 5762 2.99 - 3.63: 21890 3.63 - 4.26: 33094 4.26 - 4.90: 47127 Nonbonded interactions: 107900 Sorted by model distance: nonbonded pdb=" CD1 LEU G 23 " pdb=" OE1 GLU G 56 " model vdw 1.717 3.460 nonbonded pdb=" N GLN G 24 " pdb=" OE2 GLU G 56 " model vdw 2.100 3.120 nonbonded pdb=" O2 DC I 49 " pdb=" N2 DG J 121 " model vdw 2.194 2.496 nonbonded pdb=" OG1 THR G 16 " pdb=" OP1 DA J 55 " model vdw 2.195 3.040 nonbonded pdb=" OG SER D 84 " pdb=" OP1 DG I 38 " model vdw 2.223 3.040 ... (remaining 107895 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'E' and resid 38 through 134) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 118) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 121) selection = (chain 'H' and resid 28 through 121) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.210 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.090 Set scattering table: 0.110 Process input model: 32.550 Find NCS groups from input model: 0.290 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 13264 Z= 0.213 Angle : 0.687 8.646 19238 Z= 0.435 Chirality : 0.038 0.228 2184 Planarity : 0.005 0.045 1361 Dihedral : 27.461 88.908 5745 Min Nonbonded Distance : 1.717 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.47 % Favored : 98.53 % Rotamer: Outliers : 0.31 % Allowed : 1.10 % Favored : 98.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.28), residues: 746 helix: 1.00 (0.20), residues: 549 sheet: None (None), residues: 0 loop : -0.46 (0.40), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS E 113 PHE 0.015 0.002 PHE G 25 TYR 0.026 0.002 TYR B 88 ARG 0.005 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 191 time to evaluate : 0.973 Fit side-chains revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8914 (tm-30) cc_final: 0.8406 (tm-30) REVERT: B 49 LEU cc_start: 0.9175 (mt) cc_final: 0.8923 (mt) REVERT: B 53 GLU cc_start: 0.8655 (mp0) cc_final: 0.8427 (mp0) REVERT: C 90 ASP cc_start: 0.8518 (t0) cc_final: 0.8211 (t70) REVERT: D 42 LEU cc_start: 0.9576 (tp) cc_final: 0.9318 (tp) REVERT: D 65 ASP cc_start: 0.8916 (t0) cc_final: 0.8542 (t0) REVERT: E 62 ILE cc_start: 0.9611 (tt) cc_final: 0.9371 (tt) REVERT: E 74 ILE cc_start: 0.9547 (tt) cc_final: 0.9331 (tt) REVERT: F 63 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8918 (mp0) REVERT: G 64 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8473 (tm-30) REVERT: H 45 VAL cc_start: 0.9003 (t) cc_final: 0.8748 (t) REVERT: H 65 ASP cc_start: 0.9048 (t70) cc_final: 0.8844 (t0) REVERT: H 73 GLU cc_start: 0.9031 (tp30) cc_final: 0.8540 (tp30) outliers start: 2 outliers final: 0 residues processed: 191 average time/residue: 0.2340 time to fit residues: 64.0115 Evaluate side-chains 136 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 136 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 10.0000 chunk 77 optimal weight: 7.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 7.9990 chunk 30 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 59 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 C 24 GLN C 38 ASN D 44 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8189 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 13264 Z= 0.200 Angle : 0.605 7.794 19238 Z= 0.354 Chirality : 0.035 0.204 2184 Planarity : 0.005 0.057 1361 Dihedral : 31.060 88.571 4224 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 9.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.89 % Allowed : 12.91 % Favored : 85.20 % 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: 2.19 (0.30), residues: 746 helix: 2.10 (0.22), residues: 549 sheet: None (None), residues: 0 loop : -0.38 (0.41), residues: 197 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS A 113 PHE 0.012 0.001 PHE E 67 TYR 0.021 0.002 TYR C 50 ARG 0.006 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 168 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8930 (tm-30) cc_final: 0.8472 (tm-30) REVERT: B 49 LEU cc_start: 0.9325 (mt) cc_final: 0.8704 (mt) REVERT: B 53 GLU cc_start: 0.8855 (mp0) cc_final: 0.8492 (mp0) REVERT: B 63 GLU cc_start: 0.8951 (OUTLIER) cc_final: 0.8529 (mp0) REVERT: B 88 TYR cc_start: 0.8786 (m-10) cc_final: 0.8410 (m-10) REVERT: C 36 LYS cc_start: 0.9481 (ttmt) cc_final: 0.9275 (ttmm) REVERT: C 90 ASP cc_start: 0.8694 (t0) cc_final: 0.8476 (t70) REVERT: D 65 ASP cc_start: 0.8894 (t0) cc_final: 0.8627 (t0) REVERT: D 68 GLU cc_start: 0.8794 (tm-30) cc_final: 0.8400 (tm-30) REVERT: E 61 LEU cc_start: 0.9406 (mp) cc_final: 0.9149 (mp) REVERT: F 93 GLN cc_start: 0.9306 (tp40) cc_final: 0.9036 (tp40) REVERT: G 64 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8871 (tm-30) REVERT: H 65 ASP cc_start: 0.9103 (t70) cc_final: 0.8884 (t0) REVERT: H 73 GLU cc_start: 0.9084 (tp30) cc_final: 0.8735 (tp30) REVERT: H 80 TYR cc_start: 0.7589 (m-10) cc_final: 0.6344 (m-10) outliers start: 12 outliers final: 3 residues processed: 175 average time/residue: 0.2194 time to fit residues: 56.8038 Evaluate side-chains 140 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 136 time to evaluate : 0.861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 70 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain E residue 109 LEU Chi-restraints excluded: chain G residue 78 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 2.9990 chunk 25 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 100 optimal weight: 7.9990 chunk 82 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 6.9990 chunk 91 optimal weight: 7.9990 overall best weight: 2.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 24 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.4696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 13264 Z= 0.293 Angle : 0.664 12.319 19238 Z= 0.383 Chirality : 0.038 0.176 2184 Planarity : 0.005 0.054 1361 Dihedral : 31.946 89.857 4224 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.74 % Favored : 98.26 % Rotamer: Outliers : 4.25 % Allowed : 14.65 % Favored : 81.10 % 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: 2.16 (0.30), residues: 746 helix: 2.07 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.39 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 75 PHE 0.030 0.003 PHE E 67 TYR 0.037 0.002 TYR F 88 ARG 0.005 0.001 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 177 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 150 time to evaluate : 0.891 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 94 GLU cc_start: 0.9164 (tp30) cc_final: 0.8520 (tp30) REVERT: A 97 GLU cc_start: 0.8424 (mt-10) cc_final: 0.8200 (mt-10) REVERT: A 105 GLU cc_start: 0.8913 (tm-30) cc_final: 0.8592 (tm-30) REVERT: A 120 MET cc_start: 0.8942 (mmm) cc_final: 0.8706 (mmm) REVERT: B 46 ILE cc_start: 0.9775 (OUTLIER) cc_final: 0.9528 (pt) REVERT: B 53 GLU cc_start: 0.9122 (mp0) cc_final: 0.8680 (mp0) REVERT: B 63 GLU cc_start: 0.8880 (OUTLIER) cc_final: 0.8567 (mp0) REVERT: B 74 GLU cc_start: 0.8655 (mt-10) cc_final: 0.8448 (mt-10) REVERT: B 88 TYR cc_start: 0.9047 (m-10) cc_final: 0.8696 (m-10) REVERT: C 36 LYS cc_start: 0.9609 (ttmt) cc_final: 0.9390 (ttmm) REVERT: C 61 GLU cc_start: 0.8939 (OUTLIER) cc_final: 0.8609 (mm-30) REVERT: C 64 GLU cc_start: 0.9102 (OUTLIER) cc_final: 0.8821 (pp20) REVERT: D 65 ASP cc_start: 0.8940 (t0) cc_final: 0.8649 (t0) REVERT: D 68 GLU cc_start: 0.8876 (tm-30) cc_final: 0.8653 (tm-30) REVERT: D 83 ARG cc_start: 0.9064 (tpp80) cc_final: 0.8714 (tpp80) REVERT: E 120 MET cc_start: 0.8111 (mpp) cc_final: 0.7731 (mpp) REVERT: F 53 GLU cc_start: 0.9397 (OUTLIER) cc_final: 0.9137 (mp0) REVERT: G 104 GLN cc_start: 0.9049 (mp10) cc_final: 0.8678 (pm20) REVERT: H 65 ASP cc_start: 0.9095 (t70) cc_final: 0.8867 (t0) outliers start: 27 outliers final: 11 residues processed: 161 average time/residue: 0.2511 time to fit residues: 57.3116 Evaluate side-chains 138 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 122 time to evaluate : 0.881 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 22 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain F residue 53 GLU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain H residue 51 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 0.7980 chunk 48 optimal weight: 4.9990 chunk 10 optimal weight: 2.9990 chunk 44 optimal weight: 0.9990 chunk 62 optimal weight: 2.9990 chunk 93 optimal weight: 8.9990 chunk 98 optimal weight: 6.9990 chunk 88 optimal weight: 10.0000 chunk 26 optimal weight: 3.9990 chunk 82 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 overall best weight: 2.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8633 moved from start: 0.5362 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13264 Z= 0.257 Angle : 0.625 9.862 19238 Z= 0.362 Chirality : 0.035 0.142 2184 Planarity : 0.004 0.055 1361 Dihedral : 31.661 88.824 4224 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.05 % Allowed : 20.16 % Favored : 77.80 % 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: 2.34 (0.30), residues: 746 helix: 2.23 (0.22), residues: 550 sheet: None (None), residues: 0 loop : -0.41 (0.42), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.006 0.001 PHE A 104 TYR 0.020 0.002 TYR F 88 ARG 0.004 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.665 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8998 (tm-30) cc_final: 0.8688 (tm-30) REVERT: A 120 MET cc_start: 0.8972 (mmm) cc_final: 0.8674 (mmm) REVERT: B 53 GLU cc_start: 0.9116 (mp0) cc_final: 0.8764 (mp0) REVERT: B 63 GLU cc_start: 0.8978 (OUTLIER) cc_final: 0.8650 (mp0) REVERT: B 74 GLU cc_start: 0.8485 (mt-10) cc_final: 0.8284 (mt-10) REVERT: B 84 MET cc_start: 0.9361 (mmm) cc_final: 0.8911 (mmm) REVERT: B 88 TYR cc_start: 0.9061 (m-10) cc_final: 0.8671 (m-10) REVERT: C 36 LYS cc_start: 0.9612 (ttmt) cc_final: 0.9378 (ttmm) REVERT: C 61 GLU cc_start: 0.8936 (OUTLIER) cc_final: 0.8464 (mm-30) REVERT: C 64 GLU cc_start: 0.9134 (tm-30) cc_final: 0.8827 (pp20) REVERT: D 65 ASP cc_start: 0.8983 (t0) cc_final: 0.8725 (t0) REVERT: D 68 GLU cc_start: 0.8885 (tm-30) cc_final: 0.8622 (tm-30) REVERT: D 83 ARG cc_start: 0.9064 (tpp80) cc_final: 0.8664 (tpp80) REVERT: E 120 MET cc_start: 0.7993 (mpp) cc_final: 0.7548 (mpp) REVERT: G 61 GLU cc_start: 0.8883 (mm-30) cc_final: 0.8674 (mm-30) REVERT: G 64 GLU cc_start: 0.9283 (tm-30) cc_final: 0.9059 (pp20) REVERT: G 72 ASP cc_start: 0.8896 (m-30) cc_final: 0.8657 (p0) REVERT: G 104 GLN cc_start: 0.8960 (mp10) cc_final: 0.8439 (mp10) REVERT: H 73 GLU cc_start: 0.9212 (tp30) cc_final: 0.8752 (tp30) REVERT: H 102 GLU cc_start: 0.8501 (tp30) cc_final: 0.8056 (tp30) outliers start: 13 outliers final: 6 residues processed: 141 average time/residue: 0.2530 time to fit residues: 52.5036 Evaluate side-chains 125 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 0.9990 chunk 73 optimal weight: 8.9990 chunk 40 optimal weight: 5.9990 chunk 84 optimal weight: 8.9990 chunk 68 optimal weight: 8.9990 chunk 0 optimal weight: 9.9990 chunk 50 optimal weight: 2.9990 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 overall best weight: 1.7788 ------------------------------------------------------------------------------- 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** D 60 ASN F 75 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8643 moved from start: 0.5709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13264 Z= 0.230 Angle : 0.614 9.806 19238 Z= 0.354 Chirality : 0.034 0.159 2184 Planarity : 0.004 0.053 1361 Dihedral : 31.574 89.460 4224 Min Nonbonded Distance : 2.079 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 2.05 % Allowed : 22.05 % Favored : 75.91 % 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: 2.56 (0.31), residues: 746 helix: 2.39 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.25 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.016 0.001 PHE E 67 TYR 0.023 0.001 TYR F 88 ARG 0.005 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 128 time to evaluate : 0.805 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 105 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8675 (tm-30) REVERT: B 53 GLU cc_start: 0.9106 (mp0) cc_final: 0.8712 (mp0) REVERT: B 63 GLU cc_start: 0.8949 (OUTLIER) cc_final: 0.8617 (mp0) REVERT: B 74 GLU cc_start: 0.8522 (mt-10) cc_final: 0.8276 (mt-10) REVERT: B 84 MET cc_start: 0.9344 (mmm) cc_final: 0.8901 (mmm) REVERT: B 88 TYR cc_start: 0.9022 (m-10) cc_final: 0.8589 (m-10) REVERT: C 61 GLU cc_start: 0.9014 (OUTLIER) cc_final: 0.8752 (mm-30) REVERT: D 65 ASP cc_start: 0.8933 (t0) cc_final: 0.8718 (t0) REVERT: D 68 GLU cc_start: 0.8884 (tm-30) cc_final: 0.8598 (tm-30) REVERT: D 83 ARG cc_start: 0.9109 (tpp80) cc_final: 0.8689 (tpp80) REVERT: E 120 MET cc_start: 0.8137 (mpp) cc_final: 0.7746 (mpp) REVERT: F 88 TYR cc_start: 0.8528 (m-80) cc_final: 0.7168 (m-80) REVERT: G 61 GLU cc_start: 0.8932 (mm-30) cc_final: 0.8652 (mm-30) REVERT: G 104 GLN cc_start: 0.9007 (mp10) cc_final: 0.8672 (mp10) REVERT: H 80 TYR cc_start: 0.7056 (m-10) cc_final: 0.6508 (m-10) REVERT: H 102 GLU cc_start: 0.8348 (tp30) cc_final: 0.8014 (tp30) outliers start: 13 outliers final: 6 residues processed: 135 average time/residue: 0.2313 time to fit residues: 45.4001 Evaluate side-chains 125 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 117 time to evaluate : 0.938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 98 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 45 optimal weight: 0.0470 chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 2.9990 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 chunk 11 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 overall best weight: 1.5682 ------------------------------------------------------------------------------- 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** D 60 ASN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8644 moved from start: 0.6004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13264 Z= 0.217 Angle : 0.625 14.042 19238 Z= 0.356 Chirality : 0.034 0.221 2184 Planarity : 0.004 0.052 1361 Dihedral : 31.494 89.393 4224 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 2.36 % Allowed : 21.89 % Favored : 75.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.48 (0.31), residues: 746 helix: 2.33 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.27 (0.42), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 113 PHE 0.021 0.002 PHE E 67 TYR 0.012 0.001 TYR F 88 ARG 0.006 0.000 ARG B 23 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 133 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8976 (tm-30) cc_final: 0.8666 (tm-30) REVERT: A 120 MET cc_start: 0.8849 (mmm) cc_final: 0.8476 (mmm) REVERT: B 53 GLU cc_start: 0.9105 (mp0) cc_final: 0.8739 (mp0) REVERT: B 63 GLU cc_start: 0.8961 (OUTLIER) cc_final: 0.8603 (mp0) REVERT: B 74 GLU cc_start: 0.8501 (mt-10) cc_final: 0.8229 (mt-10) REVERT: B 84 MET cc_start: 0.9328 (mmm) cc_final: 0.8898 (mmm) REVERT: B 88 TYR cc_start: 0.9028 (m-10) cc_final: 0.8551 (m-10) REVERT: C 39 TYR cc_start: 0.9485 (m-80) cc_final: 0.9263 (m-80) REVERT: C 61 GLU cc_start: 0.8991 (OUTLIER) cc_final: 0.8624 (mm-30) REVERT: D 68 GLU cc_start: 0.8905 (tm-30) cc_final: 0.8615 (tm-30) REVERT: D 83 ARG cc_start: 0.9112 (tpp80) cc_final: 0.8674 (tpp80) REVERT: E 65 LEU cc_start: 0.9859 (OUTLIER) cc_final: 0.9541 (mm) REVERT: E 105 GLU cc_start: 0.8976 (tp30) cc_final: 0.8684 (tm-30) REVERT: E 120 MET cc_start: 0.8167 (mpp) cc_final: 0.7848 (mpp) REVERT: F 59 LYS cc_start: 0.9553 (tttm) cc_final: 0.8902 (tptm) REVERT: F 63 GLU cc_start: 0.9256 (mt-10) cc_final: 0.8552 (mt-10) REVERT: F 88 TYR cc_start: 0.8645 (m-80) cc_final: 0.7858 (m-80) REVERT: G 61 GLU cc_start: 0.8971 (mm-30) cc_final: 0.8580 (mm-30) REVERT: G 64 GLU cc_start: 0.9324 (tm-30) cc_final: 0.9064 (pp20) REVERT: G 104 GLN cc_start: 0.8899 (mp10) cc_final: 0.8578 (mp10) REVERT: H 73 GLU cc_start: 0.9157 (tp30) cc_final: 0.8655 (tp30) REVERT: H 80 TYR cc_start: 0.7054 (m-10) cc_final: 0.6659 (m-10) REVERT: H 102 GLU cc_start: 0.8340 (tp30) cc_final: 0.7915 (tp30) outliers start: 15 outliers final: 8 residues processed: 142 average time/residue: 0.2351 time to fit residues: 48.3048 Evaluate side-chains 131 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 120 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain D residue 103 LEU Chi-restraints excluded: chain E residue 62 ILE Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 10.0000 chunk 55 optimal weight: 0.9980 chunk 83 optimal weight: 7.9990 chunk 98 optimal weight: 7.9990 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 0.5980 chunk 45 optimal weight: 5.9990 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 8.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- 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** C 31 HIS D 60 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.6312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13264 Z= 0.218 Angle : 0.631 13.512 19238 Z= 0.358 Chirality : 0.034 0.183 2184 Planarity : 0.004 0.051 1361 Dihedral : 31.459 88.719 4224 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.83 % Allowed : 22.36 % Favored : 74.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.45 (0.31), residues: 746 helix: 2.32 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.30 (0.43), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.011 0.001 PHE E 67 TYR 0.011 0.001 TYR F 88 ARG 0.002 0.000 ARG H 83 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 127 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8956 (tm-30) cc_final: 0.8651 (tm-30) REVERT: A 120 MET cc_start: 0.8932 (mmm) cc_final: 0.8573 (mmm) REVERT: B 53 GLU cc_start: 0.9133 (mp0) cc_final: 0.8700 (mp0) REVERT: B 63 GLU cc_start: 0.8970 (OUTLIER) cc_final: 0.8616 (mp0) REVERT: B 74 GLU cc_start: 0.8480 (mt-10) cc_final: 0.8182 (mt-10) REVERT: B 84 MET cc_start: 0.9318 (mmm) cc_final: 0.8898 (mmm) REVERT: B 88 TYR cc_start: 0.9030 (m-10) cc_final: 0.8566 (m-10) REVERT: C 61 GLU cc_start: 0.9018 (OUTLIER) cc_final: 0.8489 (mm-30) REVERT: C 64 GLU cc_start: 0.9144 (tm-30) cc_final: 0.8883 (pp20) REVERT: D 68 GLU cc_start: 0.8929 (tm-30) cc_final: 0.8666 (tm-30) REVERT: D 83 ARG cc_start: 0.9132 (tpp80) cc_final: 0.8688 (tpp80) REVERT: E 105 GLU cc_start: 0.9025 (tp30) cc_final: 0.8667 (tm-30) REVERT: E 120 MET cc_start: 0.8191 (mpp) cc_final: 0.7991 (mtt) REVERT: F 59 LYS cc_start: 0.9539 (tttm) cc_final: 0.8865 (tptm) REVERT: F 63 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8531 (mt-10) REVERT: F 88 TYR cc_start: 0.8658 (m-80) cc_final: 0.7706 (m-80) REVERT: G 61 GLU cc_start: 0.8972 (mm-30) cc_final: 0.8596 (mm-30) REVERT: G 64 GLU cc_start: 0.9286 (tm-30) cc_final: 0.9083 (pp20) REVERT: G 104 GLN cc_start: 0.8927 (mp10) cc_final: 0.8363 (mp10) REVERT: H 80 TYR cc_start: 0.6887 (m-10) cc_final: 0.6541 (m-10) REVERT: H 102 GLU cc_start: 0.8399 (tp30) cc_final: 0.8060 (tp30) REVERT: H 103 LEU cc_start: 0.9528 (mt) cc_final: 0.9325 (mp) outliers start: 18 outliers final: 8 residues processed: 140 average time/residue: 0.2329 time to fit residues: 47.4606 Evaluate side-chains 130 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 120 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 4.9990 chunk 62 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 89 optimal weight: 7.9990 chunk 94 optimal weight: 7.9990 chunk 85 optimal weight: 9.9990 chunk 91 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 overall best weight: 4.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 38 ASN F 27 GLN G 38 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8761 moved from start: 0.7086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 13264 Z= 0.421 Angle : 0.718 13.243 19238 Z= 0.407 Chirality : 0.038 0.246 2184 Planarity : 0.005 0.065 1361 Dihedral : 32.099 89.365 4224 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 13.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 2.99 % Allowed : 22.83 % Favored : 74.17 % 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 (0.30), residues: 746 helix: 2.13 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.63 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 75 PHE 0.042 0.003 PHE E 67 TYR 0.012 0.002 TYR C 50 ARG 0.004 0.001 ARG B 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 113 time to evaluate : 0.960 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8962 (tm-30) cc_final: 0.8642 (tm-30) REVERT: A 120 MET cc_start: 0.9016 (mmm) cc_final: 0.8654 (mmm) REVERT: B 53 GLU cc_start: 0.9110 (mp0) cc_final: 0.8731 (mp0) REVERT: B 63 GLU cc_start: 0.8942 (OUTLIER) cc_final: 0.8631 (mp0) REVERT: B 74 GLU cc_start: 0.8624 (mt-10) cc_final: 0.8334 (mt-10) REVERT: B 88 TYR cc_start: 0.9051 (m-10) cc_final: 0.8610 (m-10) REVERT: C 38 ASN cc_start: 0.9357 (OUTLIER) cc_final: 0.8317 (t0) REVERT: C 61 GLU cc_start: 0.8931 (OUTLIER) cc_final: 0.8512 (mp0) REVERT: C 64 GLU cc_start: 0.9153 (tm-30) cc_final: 0.8889 (pp20) REVERT: D 68 GLU cc_start: 0.8985 (tm-30) cc_final: 0.8761 (tm-30) REVERT: D 83 ARG cc_start: 0.9278 (tpp80) cc_final: 0.8790 (tpp80) REVERT: E 65 LEU cc_start: 0.9860 (OUTLIER) cc_final: 0.9563 (mm) REVERT: E 97 GLU cc_start: 0.8257 (mt-10) cc_final: 0.7711 (mt-10) REVERT: E 105 GLU cc_start: 0.9027 (tp30) cc_final: 0.8739 (tm-30) REVERT: E 120 MET cc_start: 0.8297 (mpp) cc_final: 0.7975 (mtt) REVERT: F 59 LYS cc_start: 0.9551 (tttm) cc_final: 0.8945 (tptm) REVERT: F 63 GLU cc_start: 0.9264 (mt-10) cc_final: 0.8612 (mt-10) REVERT: F 88 TYR cc_start: 0.8765 (m-80) cc_final: 0.6837 (m-80) REVERT: G 38 ASN cc_start: 0.9082 (OUTLIER) cc_final: 0.7338 (t0) REVERT: G 56 GLU cc_start: 0.8965 (mt-10) cc_final: 0.8650 (mm-30) REVERT: G 61 GLU cc_start: 0.9126 (mm-30) cc_final: 0.8728 (mm-30) REVERT: G 64 GLU cc_start: 0.9355 (tm-30) cc_final: 0.9135 (pp20) REVERT: G 104 GLN cc_start: 0.9050 (mp10) cc_final: 0.8437 (mp10) REVERT: H 102 GLU cc_start: 0.8578 (tp30) cc_final: 0.8170 (tp30) outliers start: 19 outliers final: 12 residues processed: 127 average time/residue: 0.2401 time to fit residues: 45.0376 Evaluate side-chains 127 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.802 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 91 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 0.7980 chunk 71 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 82 optimal weight: 6.9990 chunk 86 optimal weight: 20.0000 chunk 91 optimal weight: 7.9990 chunk 60 optimal weight: 3.9990 chunk 96 optimal weight: 6.9990 chunk 59 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 chunk 67 optimal weight: 0.0870 overall best weight: 1.1362 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8697 moved from start: 0.7072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13264 Z= 0.216 Angle : 0.661 12.000 19238 Z= 0.373 Chirality : 0.035 0.225 2184 Planarity : 0.004 0.060 1361 Dihedral : 31.655 88.757 4224 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 10.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 1.89 % Allowed : 24.41 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.21 (0.31), residues: 746 helix: 2.19 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.56 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS A 113 PHE 0.052 0.002 PHE E 67 TYR 0.031 0.002 TYR H 80 ARG 0.002 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 124 time to evaluate : 1.034 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8971 (tm-30) cc_final: 0.8654 (tm-30) REVERT: A 120 MET cc_start: 0.8887 (mmm) cc_final: 0.8539 (mmm) REVERT: B 53 GLU cc_start: 0.9127 (mp0) cc_final: 0.8681 (mp0) REVERT: B 59 LYS cc_start: 0.9157 (tppp) cc_final: 0.8698 (tppt) REVERT: B 63 GLU cc_start: 0.8959 (OUTLIER) cc_final: 0.8598 (mp0) REVERT: B 88 TYR cc_start: 0.9049 (m-10) cc_final: 0.8536 (m-10) REVERT: C 61 GLU cc_start: 0.9048 (OUTLIER) cc_final: 0.8572 (mm-30) REVERT: C 64 GLU cc_start: 0.9146 (tm-30) cc_final: 0.8877 (pp20) REVERT: D 68 GLU cc_start: 0.8943 (tm-30) cc_final: 0.8674 (tm-30) REVERT: D 83 ARG cc_start: 0.9221 (tpp80) cc_final: 0.8658 (tpp80) REVERT: E 65 LEU cc_start: 0.9832 (OUTLIER) cc_final: 0.9560 (mm) REVERT: E 94 GLU cc_start: 0.9080 (tt0) cc_final: 0.8873 (tp30) REVERT: E 105 GLU cc_start: 0.9020 (tp30) cc_final: 0.8731 (tm-30) REVERT: E 120 MET cc_start: 0.8306 (mpp) cc_final: 0.7938 (mtt) REVERT: F 59 LYS cc_start: 0.9537 (tttm) cc_final: 0.9146 (tptm) REVERT: F 63 GLU cc_start: 0.9252 (mt-10) cc_final: 0.8294 (mt-10) REVERT: G 56 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8609 (mm-30) REVERT: G 61 GLU cc_start: 0.8981 (mm-30) cc_final: 0.8563 (mm-30) REVERT: G 104 GLN cc_start: 0.8857 (mp10) cc_final: 0.8507 (mp10) REVERT: H 73 GLU cc_start: 0.9181 (tp30) cc_final: 0.8551 (tp30) REVERT: H 102 GLU cc_start: 0.8540 (tp30) cc_final: 0.8106 (tp30) outliers start: 12 outliers final: 7 residues processed: 132 average time/residue: 0.2430 time to fit residues: 46.2901 Evaluate side-chains 128 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 118 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 91 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 10.0000 chunk 93 optimal weight: 7.9990 chunk 80 optimal weight: 8.9990 chunk 8 optimal weight: 0.5980 chunk 62 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 chunk 64 optimal weight: 0.9980 chunk 86 optimal weight: 20.0000 chunk 24 optimal weight: 7.9990 chunk 74 optimal weight: 8.9990 chunk 11 optimal weight: 3.9990 overall best weight: 2.7186 ------------------------------------------------------------------------------- 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** G 38 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8735 moved from start: 0.7358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 13264 Z= 0.294 Angle : 0.686 13.638 19238 Z= 0.385 Chirality : 0.036 0.217 2184 Planarity : 0.004 0.059 1361 Dihedral : 31.809 88.912 4224 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 1.89 % Allowed : 23.94 % Favored : 74.17 % 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 (0.30), residues: 746 helix: 2.15 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.69 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.046 0.002 PHE E 67 TYR 0.028 0.002 TYR H 80 ARG 0.003 0.000 ARG B 67 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1492 Ramachandran restraints generated. 746 Oldfield, 0 Emsley, 746 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 120 time to evaluate : 0.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8977 (tm-30) cc_final: 0.8669 (tm-30) REVERT: A 120 MET cc_start: 0.8979 (mmm) cc_final: 0.8626 (mmm) REVERT: B 53 GLU cc_start: 0.9109 (mp0) cc_final: 0.8715 (mp0) REVERT: B 59 LYS cc_start: 0.9171 (tppp) cc_final: 0.8746 (ttmm) REVERT: B 63 GLU cc_start: 0.8940 (OUTLIER) cc_final: 0.8624 (mp0) REVERT: B 88 TYR cc_start: 0.9051 (m-10) cc_final: 0.8529 (m-10) REVERT: C 61 GLU cc_start: 0.8937 (OUTLIER) cc_final: 0.8467 (mp0) REVERT: C 64 GLU cc_start: 0.9173 (tm-30) cc_final: 0.8860 (pp20) REVERT: D 68 GLU cc_start: 0.8964 (tm-30) cc_final: 0.8714 (tm-30) REVERT: D 83 ARG cc_start: 0.9279 (tpp80) cc_final: 0.9025 (tpp80) REVERT: E 65 LEU cc_start: 0.9836 (OUTLIER) cc_final: 0.9544 (mm) REVERT: E 97 GLU cc_start: 0.8348 (mt-10) cc_final: 0.7878 (mt-10) REVERT: E 105 GLU cc_start: 0.9030 (tp30) cc_final: 0.8739 (tm-30) REVERT: E 120 MET cc_start: 0.8335 (mpp) cc_final: 0.7967 (mtt) REVERT: F 59 LYS cc_start: 0.9525 (tttm) cc_final: 0.9146 (tptm) REVERT: F 63 GLU cc_start: 0.9251 (mt-10) cc_final: 0.8332 (mt-10) REVERT: G 38 ASN cc_start: 0.8945 (OUTLIER) cc_final: 0.8326 (t0) REVERT: G 56 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8622 (mm-30) REVERT: G 61 GLU cc_start: 0.9027 (mm-30) cc_final: 0.8632 (mm-30) REVERT: G 104 GLN cc_start: 0.8848 (mp10) cc_final: 0.8401 (mp10) REVERT: H 102 GLU cc_start: 0.8531 (tp30) cc_final: 0.8118 (tp30) outliers start: 12 outliers final: 6 residues processed: 128 average time/residue: 0.2346 time to fit residues: 43.6681 Evaluate side-chains 126 residues out of total 635 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 116 time to evaluate : 0.975 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 101 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 91 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 2.9990 chunk 81 optimal weight: 7.9990 chunk 33 optimal weight: 0.6980 chunk 83 optimal weight: 7.9990 chunk 10 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.9990 chunk 58 optimal weight: 8.9990 chunk 92 optimal weight: 7.9990 chunk 54 optimal weight: 1.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- 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** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3078 r_free = 0.3078 target = 0.038658 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2579 r_free = 0.2579 target = 0.027720 restraints weight = 136936.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.2616 r_free = 0.2616 target = 0.028330 restraints weight = 66753.293| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.2636 r_free = 0.2636 target = 0.028657 restraints weight = 42965.740| |-----------------------------------------------------------------------------| r_work (final): 0.2563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8757 moved from start: 0.7346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 13264 Z= 0.290 Angle : 0.900 58.670 19238 Z= 0.539 Chirality : 0.035 0.203 2184 Planarity : 0.004 0.059 1361 Dihedral : 31.816 88.971 4224 Min Nonbonded Distance : 2.080 Molprobity Statistics. All-atom Clashscore : 12.39 Ramachandran Plot: Outliers : 0.13 % Allowed : 2.28 % Favored : 97.59 % Rotamer: Outliers : 1.89 % Allowed : 24.25 % Favored : 73.86 % Cbeta Deviations : 0.14 % 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: 2.07 (0.30), residues: 746 helix: 2.14 (0.22), residues: 544 sheet: None (None), residues: 0 loop : -0.80 (0.40), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 75 PHE 0.037 0.002 PHE E 67 TYR 0.029 0.002 TYR H 80 ARG 0.003 0.000 ARG B 67 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2022.62 seconds wall clock time: 40 minutes 39.62 seconds (2439.62 seconds total)