Starting phenix.real_space_refine on Mon Mar 18 13:11:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/03_2024/6j99_9783_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/03_2024/6j99_9783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/03_2024/6j99_9783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/03_2024/6j99_9783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/03_2024/6j99_9783_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/03_2024/6j99_9783_updated.pdb" } resolution = 4.1 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= 0.010 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 5830 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 289 5.49 5 S 29 5.16 5 C 8711 2.51 5 N 2824 2.21 5 O 3413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 15266 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2665 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Time building chain proxies: 8.33, per 1000 atoms: 0.55 Number of scatterers: 15266 At special positions: 0 Unit cell: (132.6, 137.8, 114.4, 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 29 16.00 P 289 15.00 O 3413 8.00 N 2824 7.00 C 8711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 7.88 Conformation dependent library (CDL) restraints added in 1.7 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 49 helices and 4 sheets defined 54.9% alpha, 2.1% beta 143 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 7.97 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 removed outlier: 4.928A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 64 through 76 Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.794A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 20 No H-bonds generated for 'chain 'C' and resid 17 through 20' Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 72 removed outlier: 4.347A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 89 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 35 through 45 Processing helix chain 'D' and resid 53 through 81 Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 102 through 119 removed outlier: 3.973A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 45 through 56 removed outlier: 4.928A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 131 Processing helix chain 'F' and resid 25 through 28 No H-bonds generated for 'chain 'F' and resid 25 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 49 through 75 removed outlier: 3.749A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.651A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 35 through 45 Processing helix chain 'H' and resid 53 through 80 Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 101 through 120 Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'K' and resid 33 through 46 removed outlier: 3.548A pdb=" N ILE K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 52 through 55 No H-bonds generated for 'chain 'K' and resid 52 through 55' Processing helix chain 'K' and resid 68 through 89 Processing helix chain 'K' and resid 104 through 118 Processing helix chain 'K' and resid 122 through 126 Processing helix chain 'K' and resid 141 through 150 Processing helix chain 'K' and resid 168 through 176 Processing helix chain 'K' and resid 189 through 208 Processing helix chain 'K' and resid 226 through 234 Processing helix chain 'K' and resid 242 through 244 No H-bonds generated for 'chain 'K' and resid 242 through 244' Processing helix chain 'K' and resid 247 through 259 removed outlier: 4.399A pdb=" N ASN K 259 " --> pdb=" O GLU K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 282 through 284 No H-bonds generated for 'chain 'K' and resid 282 through 284' Processing helix chain 'K' and resid 288 through 290 No H-bonds generated for 'chain 'K' and resid 288 through 290' Processing helix chain 'K' and resid 320 through 330 Processing sheet with id= A, first strand: chain 'L' and resid 4 through 6 Processing sheet with id= B, first strand: chain 'L' and resid 41 through 43 Processing sheet with id= C, first strand: chain 'K' and resid 159 through 161 Processing sheet with id= D, first strand: chain 'K' and resid 238 through 240 removed outlier: 3.972A pdb=" N VAL K 240 " --> pdb=" O VAL K 267 " (cutoff:3.500A) 447 hydrogen bonds defined for protein. 1335 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 5.96 Time building geometry restraints manager: 8.23 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: 2782 1.33 - 1.45: 5098 1.45 - 1.57: 7638 1.57 - 1.69: 577 1.69 - 1.81: 50 Bond restraints: 16145 Sorted by residual: bond pdb=" C8 SAH K 501 " pdb=" N7 SAH K 501 " ideal model delta sigma weight residual 1.299 1.357 -0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" C2 SAH K 501 " pdb=" N3 SAH K 501 " ideal model delta sigma weight residual 1.322 1.367 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.78e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.74e+00 bond pdb=" C LYS B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 1.337 1.361 -0.024 1.24e-02 6.50e+03 3.78e+00 ... (remaining 16140 not shown) Histogram of bond angle deviations from ideal: 90.41 - 99.15: 73 99.15 - 107.89: 2875 107.89 - 116.62: 9727 116.62 - 125.36: 9339 125.36 - 134.10: 1041 Bond angle restraints: 23055 Sorted by residual: angle pdb=" C LEU K 299 " pdb=" N LYS K 300 " pdb=" CA LYS K 300 " ideal model delta sigma weight residual 121.70 132.86 -11.16 1.80e+00 3.09e-01 3.84e+01 angle pdb=" N GLY L 75 " pdb=" CA GLY L 75 " pdb=" C GLY L 75 " ideal model delta sigma weight residual 113.18 102.30 10.88 2.37e+00 1.78e-01 2.11e+01 angle pdb=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.97 127.28 -6.31 1.48e+00 4.57e-01 1.82e+01 angle pdb=" C ARG E 49 " pdb=" N GLU E 50 " pdb=" CA GLU E 50 " ideal model delta sigma weight residual 126.45 133.50 -7.05 1.77e+00 3.19e-01 1.59e+01 angle pdb=" C ARG A 49 " pdb=" N GLU A 50 " pdb=" CA GLU A 50 " ideal model delta sigma weight residual 126.45 133.46 -7.01 1.77e+00 3.19e-01 1.57e+01 ... (remaining 23050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.05: 7058 30.05 - 60.09: 1830 60.09 - 90.14: 85 90.14 - 120.18: 1 120.18 - 150.23: 2 Dihedral angle restraints: 8976 sinusoidal: 5583 harmonic: 3393 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -145.87 -34.13 0 5.00e+00 4.00e-02 4.66e+01 dihedral pdb=" CA SER K 304 " pdb=" C SER K 304 " pdb=" N TRP K 305 " pdb=" CA TRP K 305 " ideal model delta harmonic sigma weight residual 180.00 148.77 31.23 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ARG L 74 " pdb=" C ARG L 74 " pdb=" N GLY L 75 " pdb=" CA GLY L 75 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 8973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1840 0.050 - 0.100: 620 0.100 - 0.150: 121 0.150 - 0.200: 21 0.200 - 0.250: 5 Chirality restraints: 2607 Sorted by residual: chirality pdb=" P DT J 83 " pdb=" OP1 DT J 83 " pdb=" OP2 DT J 83 " pdb=" O5' DT J 83 " both_signs ideal model delta sigma weight residual True 2.35 -2.60 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C1' DG J 82 " pdb=" O4' DG J 82 " pdb=" C2' DG J 82 " pdb=" N9 DG J 82 " both_signs ideal model delta sigma weight residual False 2.42 2.18 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE L 13 " pdb=" CA ILE L 13 " pdb=" CG1 ILE L 13 " pdb=" CG2 ILE L 13 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2604 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 45 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.22e+00 pdb=" C THR E 45 " -0.050 2.00e-02 2.50e+03 pdb=" O THR E 45 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL E 46 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 50 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C GLU A 50 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU A 50 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 51 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 50 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C GLU E 50 " 0.049 2.00e-02 2.50e+03 pdb=" O GLU E 50 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE E 51 " -0.017 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1905 2.74 - 3.28: 14319 3.28 - 3.82: 32287 3.82 - 4.36: 36137 4.36 - 4.90: 51800 Nonbonded interactions: 136448 Sorted by model distance: nonbonded pdb=" OD1 ASP A 123 " pdb=" NE2 HIS E 113 " model vdw 2.204 2.520 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.250 2.440 nonbonded pdb=" OD1 ASN K 242 " pdb=" OG SER K 269 " model vdw 2.252 2.440 nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.260 2.496 nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 122 " model vdw 2.271 2.440 ... (remaining 136443 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 2.600 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 48.600 Find NCS groups from input model: 0.530 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:2.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5209 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 : 0.008 0.066 16145 Z= 0.449 Angle : 0.978 11.900 23055 Z= 0.559 Chirality : 0.051 0.250 2607 Planarity : 0.007 0.066 1920 Dihedral : 27.095 150.230 6782 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.88 (0.21), residues: 1143 helix: -1.35 (0.16), residues: 694 sheet: -3.97 (0.63), residues: 37 loop : -2.49 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP K 228 HIS 0.019 0.003 HIS C 82 PHE 0.027 0.004 PHE K 245 TYR 0.041 0.004 TYR G 39 ARG 0.008 0.001 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 379 time to evaluate : 1.129 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.5261 (mt) cc_final: 0.4326 (mt) REVERT: A 93 GLN cc_start: 0.4178 (tt0) cc_final: 0.3786 (tt0) REVERT: B 100 PHE cc_start: 0.7406 (m-80) cc_final: 0.7027 (m-10) REVERT: C 57 TYR cc_start: 0.8736 (t80) cc_final: 0.8119 (t80) REVERT: C 75 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7656 (mmtt) REVERT: D 90 GLU cc_start: 0.7424 (mp0) cc_final: 0.7194 (mp0) REVERT: D 106 HIS cc_start: 0.7983 (m-70) cc_final: 0.7287 (m-70) REVERT: G 68 ASN cc_start: 0.8396 (m-40) cc_final: 0.8053 (m-40) REVERT: G 72 ASP cc_start: 0.9244 (m-30) cc_final: 0.8830 (m-30) REVERT: G 115 LEU cc_start: 0.6386 (mt) cc_final: 0.5923 (tt) REVERT: H 90 GLU cc_start: 0.6325 (mp0) cc_final: 0.5988 (mt-10) REVERT: H 100 PRO cc_start: 0.4871 (Cg_endo) cc_final: 0.4583 (Cg_exo) REVERT: L 1 MET cc_start: 0.2615 (ttp) cc_final: 0.1893 (ttt) REVERT: L 6 LYS cc_start: 0.8999 (tttt) cc_final: 0.8754 (tptt) REVERT: L 71 LEU cc_start: 0.8587 (mp) cc_final: 0.7860 (mt) REVERT: K 53 LEU cc_start: 0.5821 (tp) cc_final: 0.5539 (pp) REVERT: K 66 LYS cc_start: 0.7634 (mppt) cc_final: 0.7178 (pttt) REVERT: K 96 MET cc_start: -0.0461 (ttp) cc_final: -0.1120 (tpt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.3840 time to fit residues: 190.8349 Evaluate side-chains 236 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 236 time to evaluate : 0.972 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 5.9990 chunk 105 optimal weight: 9.9990 chunk 58 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 71 optimal weight: 10.0000 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 0.2980 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 126 optimal weight: 5.9990 overall best weight: 0.7584 ------------------------------------------------------------------------------- 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** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS C 24 GLN C 68 ASN D 46 HIS D 79 HIS D 81 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 38 ASN G 89 ASN K 35 HIS K 126 ASN K 251 HIS K 252 GLN K 315 HIS Total number of N/Q/H flips: 14 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5456 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.084 16145 Z= 0.205 Angle : 0.676 8.721 23055 Z= 0.388 Chirality : 0.041 0.270 2607 Planarity : 0.005 0.072 1920 Dihedral : 32.054 147.858 4447 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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: -1.17 (0.24), residues: 1143 helix: 0.21 (0.18), residues: 694 sheet: -2.98 (0.64), residues: 45 loop : -2.22 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 305 HIS 0.008 0.001 HIS E 113 PHE 0.033 0.002 PHE A 104 TYR 0.014 0.002 TYR C 57 ARG 0.006 0.001 ARG K 256 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 296 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 296 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.7778 (tp30) cc_final: 0.7464 (tp30) REVERT: A 62 ILE cc_start: 0.6156 (mt) cc_final: 0.5710 (mt) REVERT: B 88 TYR cc_start: 0.8510 (m-80) cc_final: 0.8097 (m-80) REVERT: B 100 PHE cc_start: 0.7816 (m-80) cc_final: 0.7138 (m-10) REVERT: C 17 ARG cc_start: 0.7814 (mtp180) cc_final: 0.7264 (mtp85) REVERT: C 23 LEU cc_start: 0.8259 (mm) cc_final: 0.7759 (mm) REVERT: C 42 ARG cc_start: 0.6590 (mtm180) cc_final: 0.6383 (mtm-85) REVERT: C 56 GLU cc_start: 0.8565 (tp30) cc_final: 0.8187 (mm-30) REVERT: C 61 GLU cc_start: 0.8444 (mm-30) cc_final: 0.7819 (tp30) REVERT: C 75 LYS cc_start: 0.7752 (mmtp) cc_final: 0.7534 (mmtt) REVERT: D 82 LYS cc_start: 0.8953 (mtpt) cc_final: 0.8350 (mmtt) REVERT: D 86 ILE cc_start: 0.8514 (pt) cc_final: 0.8200 (pt) REVERT: D 87 THR cc_start: 0.7909 (p) cc_final: 0.7352 (p) REVERT: D 106 HIS cc_start: 0.7988 (m-70) cc_final: 0.7090 (m-70) REVERT: E 131 ARG cc_start: 0.8319 (ttm-80) cc_final: 0.7877 (tpp-160) REVERT: F 84 MET cc_start: 0.6445 (mmp) cc_final: 0.5999 (mmp) REVERT: G 82 HIS cc_start: 0.8371 (m170) cc_final: 0.8153 (m-70) REVERT: G 99 ARG cc_start: 0.6971 (mmp80) cc_final: 0.6606 (mmt180) REVERT: H 52 SER cc_start: 0.5652 (m) cc_final: 0.5242 (m) REVERT: H 76 ARG cc_start: 0.7991 (ttm-80) cc_final: 0.7771 (ttm-80) REVERT: H 100 PRO cc_start: 0.4094 (Cg_endo) cc_final: 0.3735 (Cg_exo) REVERT: L 1 MET cc_start: 0.2690 (ttp) cc_final: 0.1964 (ttt) REVERT: L 6 LYS cc_start: 0.9034 (tttt) cc_final: 0.8770 (tptt) REVERT: L 24 GLU cc_start: 0.8325 (tt0) cc_final: 0.7979 (mm-30) REVERT: L 27 LYS cc_start: 0.8395 (ptpp) cc_final: 0.8092 (mmtm) REVERT: K 66 LYS cc_start: 0.7809 (mppt) cc_final: 0.7358 (pttt) REVERT: K 96 MET cc_start: -0.0117 (ttp) cc_final: -0.0775 (tpt) REVERT: K 153 MET cc_start: 0.2585 (ttt) cc_final: 0.1786 (tmm) REVERT: K 179 CYS cc_start: 0.2940 (m) cc_final: 0.1467 (m) outliers start: 0 outliers final: 0 residues processed: 296 average time/residue: 0.3457 time to fit residues: 138.6809 Evaluate side-chains 219 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 1.210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 9.9990 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 0.6980 chunk 126 optimal weight: 7.9990 chunk 136 optimal weight: 0.7980 chunk 112 optimal weight: 5.9990 chunk 125 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 101 optimal weight: 10.0000 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 64 ASN D 79 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 57 ASN K 109 HIS K 213 HIS K 234 ASN K 241 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.5801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.081 16145 Z= 0.322 Angle : 0.818 14.381 23055 Z= 0.452 Chirality : 0.044 0.220 2607 Planarity : 0.010 0.260 1920 Dihedral : 31.821 144.428 4447 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 20.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.30 % Allowed : 5.11 % Favored : 94.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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 (0.24), residues: 1143 helix: 0.21 (0.19), residues: 694 sheet: -2.92 (0.62), residues: 55 loop : -2.01 (0.31), residues: 394 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 305 HIS 0.023 0.002 HIS K 251 PHE 0.025 0.003 PHE E 67 TYR 0.031 0.003 TYR H 37 ARG 0.010 0.001 ARG K 256 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 353 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 350 time to evaluate : 1.239 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.8248 (mt) cc_final: 0.8034 (mt) REVERT: A 120 MET cc_start: 0.6642 (mpp) cc_final: 0.6013 (mmm) REVERT: B 50 ILE cc_start: 0.5572 (mm) cc_final: 0.5304 (mm) REVERT: B 52 GLU cc_start: 0.7532 (mm-30) cc_final: 0.7062 (mp0) REVERT: B 74 GLU cc_start: 0.7854 (mm-30) cc_final: 0.7591 (mm-30) REVERT: B 88 TYR cc_start: 0.8622 (m-80) cc_final: 0.8255 (m-80) REVERT: B 100 PHE cc_start: 0.8359 (m-80) cc_final: 0.8090 (m-10) REVERT: C 75 LYS cc_start: 0.8401 (mmtp) cc_final: 0.7722 (mmmt) REVERT: C 91 GLU cc_start: 0.8568 (tm-30) cc_final: 0.8334 (tp30) REVERT: C 95 LYS cc_start: 0.9444 (tptp) cc_final: 0.9146 (tppt) REVERT: D 37 TYR cc_start: 0.8513 (m-80) cc_final: 0.7958 (m-80) REVERT: D 42 LEU cc_start: 0.8298 (tp) cc_final: 0.8031 (tp) REVERT: D 83 ARG cc_start: 0.8526 (mmp80) cc_final: 0.8260 (mmp80) REVERT: D 88 SER cc_start: 0.8699 (p) cc_final: 0.7700 (m) REVERT: D 92 GLN cc_start: 0.8449 (pt0) cc_final: 0.8202 (pm20) REVERT: D 100 PRO cc_start: 0.8399 (Cg_endo) cc_final: 0.6919 (Cg_exo) REVERT: D 106 HIS cc_start: 0.8291 (m-70) cc_final: 0.7250 (m-70) REVERT: D 110 GLU cc_start: 0.8585 (tp30) cc_final: 0.8383 (mm-30) REVERT: E 55 GLN cc_start: 0.7713 (pp30) cc_final: 0.7438 (pp30) REVERT: E 62 ILE cc_start: 0.5153 (mt) cc_final: 0.4903 (mt) REVERT: E 68 GLN cc_start: 0.7517 (pt0) cc_final: 0.7271 (pt0) REVERT: E 99 TYR cc_start: 0.8850 (t80) cc_final: 0.8270 (t80) REVERT: E 110 CYS cc_start: 0.8277 (m) cc_final: 0.7302 (m) REVERT: E 123 ASP cc_start: 0.8196 (m-30) cc_final: 0.7705 (t70) REVERT: E 125 GLN cc_start: 0.8247 (pt0) cc_final: 0.7926 (pt0) REVERT: E 134 ARG cc_start: 0.5302 (mmm160) cc_final: 0.4260 (mmm160) REVERT: F 59 LYS cc_start: 0.8877 (mmmt) cc_final: 0.8623 (mmmt) REVERT: G 71 ARG cc_start: 0.8678 (mmp80) cc_final: 0.8393 (mmp80) REVERT: G 82 HIS cc_start: 0.8675 (m170) cc_final: 0.8428 (m-70) REVERT: G 95 LYS cc_start: 0.8903 (tmmt) cc_final: 0.8376 (ttmm) REVERT: G 101 THR cc_start: 0.8953 (m) cc_final: 0.8567 (t) REVERT: H 83 ARG cc_start: 0.6746 (mmt180) cc_final: 0.5717 (mmp80) REVERT: H 103 LEU cc_start: 0.7867 (pp) cc_final: 0.7526 (pt) REVERT: L 1 MET cc_start: 0.2694 (ttp) cc_final: 0.2197 (ttt) REVERT: L 6 LYS cc_start: 0.8982 (tttt) cc_final: 0.8743 (tptp) REVERT: L 24 GLU cc_start: 0.8319 (tt0) cc_final: 0.7722 (mm-30) REVERT: L 62 GLN cc_start: 0.7689 (tp40) cc_final: 0.7412 (tp40) REVERT: K 66 LYS cc_start: 0.7966 (mppt) cc_final: 0.7549 (pttt) REVERT: K 96 MET cc_start: 0.0490 (ttp) cc_final: -0.0305 (tpp) REVERT: K 153 MET cc_start: 0.2523 (ttt) cc_final: 0.2266 (tmm) REVERT: K 170 VAL cc_start: 0.6011 (t) cc_final: 0.5569 (t) REVERT: K 179 CYS cc_start: 0.2404 (m) cc_final: 0.0482 (m) outliers start: 3 outliers final: 0 residues processed: 350 average time/residue: 0.3433 time to fit residues: 162.4229 Evaluate side-chains 272 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 272 time to evaluate : 1.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 8.9990 chunk 95 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 chunk 60 optimal weight: 0.9990 chunk 84 optimal weight: 10.0000 chunk 126 optimal weight: 3.9990 chunk 134 optimal weight: 6.9990 chunk 66 optimal weight: 0.9990 chunk 120 optimal weight: 9.9990 chunk 36 optimal weight: 8.9990 overall best weight: 1.7990 ------------------------------------------------------------------------------- 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** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 64 ASN D 79 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 31 HIS G 68 ASN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6508 moved from start: 0.6951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 16145 Z= 0.239 Angle : 0.666 9.916 23055 Z= 0.378 Chirality : 0.041 0.271 2607 Planarity : 0.005 0.064 1920 Dihedral : 31.669 145.395 4447 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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: -0.48 (0.25), residues: 1143 helix: 0.72 (0.19), residues: 691 sheet: -2.41 (0.69), residues: 53 loop : -1.84 (0.32), residues: 399 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 208 HIS 0.007 0.001 HIS K 251 PHE 0.024 0.002 PHE K 272 TYR 0.024 0.002 TYR K 312 ARG 0.009 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 332 time to evaluate : 1.289 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 31 LYS cc_start: 0.7671 (pttm) cc_final: 0.6244 (pttm) REVERT: C 72 ASP cc_start: 0.8616 (m-30) cc_final: 0.8232 (m-30) REVERT: C 75 LYS cc_start: 0.8190 (mmtp) cc_final: 0.7598 (mmmt) REVERT: C 95 LYS cc_start: 0.9472 (tptp) cc_final: 0.9000 (tppt) REVERT: D 65 ASP cc_start: 0.8964 (t70) cc_final: 0.8699 (t0) REVERT: D 83 ARG cc_start: 0.8466 (mmp80) cc_final: 0.8232 (mmp80) REVERT: D 88 SER cc_start: 0.8146 (p) cc_final: 0.7472 (m) REVERT: D 92 GLN cc_start: 0.8572 (pt0) cc_final: 0.8118 (pm20) REVERT: D 103 LEU cc_start: 0.9303 (tp) cc_final: 0.9099 (tp) REVERT: D 106 HIS cc_start: 0.8340 (m-70) cc_final: 0.7731 (m-70) REVERT: E 62 ILE cc_start: 0.5531 (mt) cc_final: 0.5071 (mt) REVERT: E 99 TYR cc_start: 0.8834 (t80) cc_final: 0.8068 (t80) REVERT: E 106 ASP cc_start: 0.8670 (m-30) cc_final: 0.8348 (m-30) REVERT: E 110 CYS cc_start: 0.8310 (m) cc_final: 0.7807 (m) REVERT: E 120 MET cc_start: 0.8292 (pmm) cc_final: 0.7919 (pmm) REVERT: E 123 ASP cc_start: 0.8262 (m-30) cc_final: 0.7653 (t70) REVERT: F 59 LYS cc_start: 0.8881 (mmmt) cc_final: 0.8581 (mmmt) REVERT: F 80 THR cc_start: 0.7259 (m) cc_final: 0.6543 (p) REVERT: F 84 MET cc_start: 0.8316 (mmp) cc_final: 0.7612 (mmm) REVERT: G 71 ARG cc_start: 0.8582 (mmp80) cc_final: 0.8211 (mmp80) REVERT: G 76 THR cc_start: 0.8971 (p) cc_final: 0.8696 (t) REVERT: G 101 THR cc_start: 0.8918 (m) cc_final: 0.8544 (t) REVERT: H 52 SER cc_start: 0.7170 (m) cc_final: 0.6542 (m) REVERT: L 1 MET cc_start: 0.2916 (ttp) cc_final: 0.2339 (ttt) REVERT: L 6 LYS cc_start: 0.8994 (tttt) cc_final: 0.8721 (tptp) REVERT: L 24 GLU cc_start: 0.8215 (tt0) cc_final: 0.7758 (mm-30) REVERT: L 27 LYS cc_start: 0.8248 (ptpp) cc_final: 0.8035 (mmtt) REVERT: L 62 GLN cc_start: 0.7610 (tp40) cc_final: 0.7347 (tp40) REVERT: K 53 LEU cc_start: 0.5928 (tp) cc_final: 0.5513 (mt) REVERT: K 66 LYS cc_start: 0.8009 (mppt) cc_final: 0.7577 (pttt) REVERT: K 96 MET cc_start: 0.0010 (ttp) cc_final: -0.0471 (tpp) REVERT: K 179 CYS cc_start: 0.2810 (m) cc_final: 0.0983 (m) REVERT: K 291 MET cc_start: 0.6732 (ptp) cc_final: 0.6331 (pmm) outliers start: 0 outliers final: 0 residues processed: 332 average time/residue: 0.3240 time to fit residues: 147.9149 Evaluate side-chains 267 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 267 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.0370 chunk 76 optimal weight: 7.9990 chunk 1 optimal weight: 10.0000 chunk 100 optimal weight: 30.0000 chunk 55 optimal weight: 3.9990 chunk 114 optimal weight: 6.9990 chunk 92 optimal weight: 7.9990 chunk 0 optimal weight: 9.9990 chunk 68 optimal weight: 0.8980 chunk 120 optimal weight: 1.9990 chunk 33 optimal weight: 0.9980 overall best weight: 1.5862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 24 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 68 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 84 GLN D 79 HIS D 81 ASN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN K 234 ASN K 241 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6735 moved from start: 0.8163 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.079 16145 Z= 0.238 Angle : 0.674 6.962 23055 Z= 0.383 Chirality : 0.040 0.244 2607 Planarity : 0.005 0.061 1920 Dihedral : 31.474 144.094 4447 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 18.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 3.11 % Favored : 96.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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: -0.36 (0.25), residues: 1143 helix: 0.82 (0.19), residues: 697 sheet: -1.93 (0.79), residues: 48 loop : -1.93 (0.30), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 305 HIS 0.009 0.001 HIS K 251 PHE 0.040 0.003 PHE E 67 TYR 0.018 0.002 TYR H 37 ARG 0.007 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 338 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 338 time to evaluate : 1.424 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 86 SER cc_start: 0.7840 (p) cc_final: 0.7302 (p) REVERT: A 89 VAL cc_start: 0.9137 (t) cc_final: 0.8923 (t) REVERT: A 93 GLN cc_start: 0.8564 (tt0) cc_final: 0.8343 (tt0) REVERT: A 116 ARG cc_start: 0.8761 (ptm160) cc_final: 0.8135 (ptm160) REVERT: A 120 MET cc_start: 0.7768 (mmm) cc_final: 0.6786 (mmm) REVERT: A 123 ASP cc_start: 0.8510 (m-30) cc_final: 0.8281 (t70) REVERT: B 52 GLU cc_start: 0.8085 (mp0) cc_final: 0.7782 (mp0) REVERT: C 15 LYS cc_start: 0.6542 (tptm) cc_final: 0.6245 (tptm) REVERT: C 75 LYS cc_start: 0.8365 (mmtp) cc_final: 0.7818 (mmmt) REVERT: C 95 LYS cc_start: 0.9403 (tptp) cc_final: 0.9071 (tppt) REVERT: D 40 LYS cc_start: 0.8865 (mttt) cc_final: 0.8539 (ttpt) REVERT: D 65 ASP cc_start: 0.8982 (t70) cc_final: 0.8666 (t0) REVERT: D 83 ARG cc_start: 0.8421 (mmp80) cc_final: 0.8106 (mmp80) REVERT: D 88 SER cc_start: 0.8384 (p) cc_final: 0.7815 (m) REVERT: D 92 GLN cc_start: 0.8674 (pt0) cc_final: 0.8263 (pm20) REVERT: D 103 LEU cc_start: 0.9341 (tp) cc_final: 0.9032 (tp) REVERT: D 106 HIS cc_start: 0.8223 (m-70) cc_final: 0.7581 (m-70) REVERT: E 90 MET cc_start: 0.8663 (tpp) cc_final: 0.8118 (tmm) REVERT: E 99 TYR cc_start: 0.9030 (t80) cc_final: 0.8488 (t80) REVERT: E 110 CYS cc_start: 0.8554 (m) cc_final: 0.8048 (m) REVERT: F 68 ASP cc_start: 0.8133 (m-30) cc_final: 0.7855 (m-30) REVERT: F 80 THR cc_start: 0.7143 (m) cc_final: 0.6870 (p) REVERT: F 84 MET cc_start: 0.8661 (mmp) cc_final: 0.8133 (mmm) REVERT: G 71 ARG cc_start: 0.8634 (mmp80) cc_final: 0.8328 (mmp80) REVERT: G 74 LYS cc_start: 0.8819 (mmpt) cc_final: 0.8616 (mmmt) REVERT: G 76 THR cc_start: 0.9090 (p) cc_final: 0.8873 (t) REVERT: G 82 HIS cc_start: 0.8646 (m170) cc_final: 0.7999 (m-70) REVERT: G 101 THR cc_start: 0.8990 (m) cc_final: 0.8691 (t) REVERT: G 104 GLN cc_start: 0.7618 (mp10) cc_final: 0.6682 (mp10) REVERT: L 1 MET cc_start: 0.3076 (ttp) cc_final: 0.1930 (tpp) REVERT: L 62 GLN cc_start: 0.7484 (tp40) cc_final: 0.7006 (tp40) REVERT: K 53 LEU cc_start: 0.5966 (tp) cc_final: 0.5525 (mt) REVERT: K 66 LYS cc_start: 0.8024 (mppt) cc_final: 0.7594 (pttt) REVERT: K 96 MET cc_start: -0.0333 (ttp) cc_final: -0.0795 (tpp) REVERT: K 147 MET cc_start: 0.4739 (mmt) cc_final: 0.4293 (mmt) REVERT: K 248 GLU cc_start: 0.8370 (mp0) cc_final: 0.7979 (mp0) REVERT: K 291 MET cc_start: 0.6829 (ptp) cc_final: 0.6589 (pmm) outliers start: 0 outliers final: 0 residues processed: 338 average time/residue: 0.3265 time to fit residues: 152.4333 Evaluate side-chains 275 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 275 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.8980 chunk 120 optimal weight: 3.9990 chunk 26 optimal weight: 4.9990 chunk 78 optimal weight: 6.9990 chunk 33 optimal weight: 0.2980 chunk 134 optimal weight: 7.9990 chunk 111 optimal weight: 8.9990 chunk 62 optimal weight: 8.9990 chunk 11 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 6.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- 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** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 79 HIS E 85 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN K 213 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7135 moved from start: 1.0053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 16145 Z= 0.298 Angle : 0.741 10.129 23055 Z= 0.413 Chirality : 0.042 0.244 2607 Planarity : 0.006 0.097 1920 Dihedral : 31.585 145.253 4447 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 21.88 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.81 % Favored : 95.10 % Rotamer: Outliers : 0.10 % Allowed : 2.91 % Favored : 96.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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: -0.34 (0.25), residues: 1143 helix: 0.83 (0.20), residues: 679 sheet: -2.10 (0.72), residues: 55 loop : -1.75 (0.30), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 305 HIS 0.008 0.001 HIS K 315 PHE 0.026 0.003 PHE B 100 TYR 0.028 0.003 TYR D 80 ARG 0.009 0.001 ARG G 42 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 359 time to evaluate : 1.202 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 65 LEU cc_start: 0.6749 (tp) cc_final: 0.6515 (tp) REVERT: A 93 GLN cc_start: 0.8794 (tt0) cc_final: 0.8319 (tt0) REVERT: A 120 MET cc_start: 0.8383 (mmm) cc_final: 0.8152 (mmm) REVERT: B 52 GLU cc_start: 0.8798 (mp0) cc_final: 0.8367 (pm20) REVERT: B 74 GLU cc_start: 0.8486 (mm-30) cc_final: 0.8007 (mt-10) REVERT: C 15 LYS cc_start: 0.6738 (tptm) cc_final: 0.6391 (tptm) REVERT: C 54 VAL cc_start: 0.9643 (m) cc_final: 0.9379 (p) REVERT: C 74 LYS cc_start: 0.8871 (mptt) cc_final: 0.8313 (mmtt) REVERT: C 75 LYS cc_start: 0.8691 (mmtp) cc_final: 0.8304 (mmmt) REVERT: C 91 GLU cc_start: 0.8278 (tm-30) cc_final: 0.7625 (tp30) REVERT: C 95 LYS cc_start: 0.9384 (tptp) cc_final: 0.9028 (tppt) REVERT: D 58 ILE cc_start: 0.9075 (mm) cc_final: 0.8734 (mm) REVERT: D 65 ASP cc_start: 0.8949 (t70) cc_final: 0.8719 (t70) REVERT: D 83 ARG cc_start: 0.8706 (mmp80) cc_final: 0.8312 (mmp80) REVERT: D 103 LEU cc_start: 0.9377 (tp) cc_final: 0.9092 (tp) REVERT: D 106 HIS cc_start: 0.8473 (m-70) cc_final: 0.7931 (m90) REVERT: D 118 TYR cc_start: 0.8969 (t80) cc_final: 0.8577 (t80) REVERT: E 51 ILE cc_start: 0.7162 (mt) cc_final: 0.6857 (mt) REVERT: E 68 GLN cc_start: 0.7906 (mp10) cc_final: 0.7700 (mp10) REVERT: E 94 GLU cc_start: 0.8645 (tm-30) cc_final: 0.8324 (tm-30) REVERT: E 99 TYR cc_start: 0.9236 (t80) cc_final: 0.8780 (t80) REVERT: F 27 GLN cc_start: 0.8264 (tp40) cc_final: 0.7947 (mp10) REVERT: F 34 ILE cc_start: 0.8609 (mt) cc_final: 0.8388 (mt) REVERT: F 36 ARG cc_start: 0.8066 (mpt-90) cc_final: 0.7638 (mtt90) REVERT: F 82 THR cc_start: 0.8266 (m) cc_final: 0.7684 (m) REVERT: G 24 GLN cc_start: 0.8199 (mm-40) cc_final: 0.6576 (mp10) REVERT: G 71 ARG cc_start: 0.8697 (mmp80) cc_final: 0.8245 (mmp80) REVERT: G 72 ASP cc_start: 0.9289 (m-30) cc_final: 0.9071 (t70) REVERT: G 76 THR cc_start: 0.8911 (p) cc_final: 0.8626 (t) REVERT: G 82 HIS cc_start: 0.8685 (m170) cc_final: 0.7958 (m-70) REVERT: G 84 GLN cc_start: 0.8868 (tp40) cc_final: 0.8577 (tp40) REVERT: G 101 THR cc_start: 0.8981 (m) cc_final: 0.8572 (t) REVERT: H 81 ASN cc_start: 0.8212 (m-40) cc_final: 0.7755 (m-40) REVERT: H 82 LYS cc_start: 0.9018 (mppt) cc_final: 0.8746 (mtmm) REVERT: H 86 ILE cc_start: 0.6710 (mm) cc_final: 0.6230 (tp) REVERT: L 1 MET cc_start: 0.3674 (ttp) cc_final: 0.2556 (tpp) REVERT: L 62 GLN cc_start: 0.7573 (tp40) cc_final: 0.7102 (tp40) REVERT: K 53 LEU cc_start: 0.6053 (tp) cc_final: 0.5600 (mt) REVERT: K 66 LYS cc_start: 0.8088 (mppt) cc_final: 0.7657 (pttt) REVERT: K 96 MET cc_start: -0.0263 (ttp) cc_final: -0.0787 (tpp) REVERT: K 147 MET cc_start: 0.4145 (mmt) cc_final: 0.3547 (mmt) REVERT: K 291 MET cc_start: 0.6919 (ptp) cc_final: 0.6659 (pmm) outliers start: 1 outliers final: 1 residues processed: 359 average time/residue: 0.3166 time to fit residues: 157.1491 Evaluate side-chains 282 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 281 time to evaluate : 1.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 76 optimal weight: 7.9990 chunk 98 optimal weight: 10.0000 chunk 113 optimal weight: 6.9990 chunk 75 optimal weight: 8.9990 chunk 133 optimal weight: 20.0000 chunk 83 optimal weight: 9.9990 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 0.9990 chunk 82 optimal weight: 8.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 64 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN K 116 ASN K 241 ASN K 315 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 1.2148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.117 16145 Z= 0.464 Angle : 0.869 12.053 23055 Z= 0.481 Chirality : 0.048 0.267 2607 Planarity : 0.007 0.077 1920 Dihedral : 31.890 146.559 4447 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 27.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.10 % Allowed : 2.51 % Favored : 97.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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 (0.24), residues: 1143 helix: 0.17 (0.19), residues: 683 sheet: -2.23 (0.71), residues: 57 loop : -2.03 (0.30), residues: 403 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 305 HIS 0.005 0.001 HIS A 113 PHE 0.050 0.004 PHE E 67 TYR 0.037 0.003 TYR D 80 ARG 0.015 0.001 ARG E 134 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 353 time to evaluate : 1.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 49 ARG cc_start: 0.8050 (ttp-110) cc_final: 0.7844 (tmm-80) REVERT: A 60 LEU cc_start: 0.9021 (mm) cc_final: 0.8769 (mt) REVERT: A 86 SER cc_start: 0.9102 (p) cc_final: 0.8845 (m) REVERT: B 52 GLU cc_start: 0.8630 (mp0) cc_final: 0.8343 (pm20) REVERT: B 55 ARG cc_start: 0.8397 (mmm160) cc_final: 0.8120 (tpt170) REVERT: B 73 THR cc_start: 0.9487 (m) cc_final: 0.9239 (t) REVERT: B 74 GLU cc_start: 0.8707 (mm-30) cc_final: 0.8297 (mt-10) REVERT: C 36 LYS cc_start: 0.9444 (mmtt) cc_final: 0.9204 (mmmt) REVERT: C 91 GLU cc_start: 0.8249 (tm-30) cc_final: 0.7780 (tp30) REVERT: C 95 LYS cc_start: 0.9516 (tptp) cc_final: 0.9127 (tppt) REVERT: D 65 ASP cc_start: 0.8972 (t70) cc_final: 0.8721 (t70) REVERT: D 82 LYS cc_start: 0.9508 (ttpt) cc_final: 0.9015 (mmtt) REVERT: D 83 ARG cc_start: 0.9010 (mmp80) cc_final: 0.8640 (mmp80) REVERT: D 103 LEU cc_start: 0.9461 (tp) cc_final: 0.9236 (tp) REVERT: D 106 HIS cc_start: 0.8306 (m-70) cc_final: 0.7731 (m90) REVERT: D 118 TYR cc_start: 0.9144 (t80) cc_final: 0.8631 (t80) REVERT: E 54 TYR cc_start: 0.7595 (m-10) cc_final: 0.7160 (m-10) REVERT: E 56 LYS cc_start: 0.8533 (mtpt) cc_final: 0.8206 (mtmm) REVERT: E 97 GLU cc_start: 0.8712 (tp30) cc_final: 0.8206 (tp30) REVERT: F 30 THR cc_start: 0.8701 (p) cc_final: 0.8288 (t) REVERT: F 36 ARG cc_start: 0.8732 (mpt-90) cc_final: 0.8221 (mtt90) REVERT: F 44 LYS cc_start: 0.7585 (pptt) cc_final: 0.7037 (pptt) REVERT: F 82 THR cc_start: 0.8313 (m) cc_final: 0.8081 (m) REVERT: F 84 MET cc_start: 0.9062 (mmp) cc_final: 0.8281 (mmm) REVERT: G 71 ARG cc_start: 0.8680 (mmp80) cc_final: 0.8240 (mmp80) REVERT: G 101 THR cc_start: 0.8911 (m) cc_final: 0.8519 (t) REVERT: G 112 GLN cc_start: 0.8887 (mm-40) cc_final: 0.8447 (mm-40) REVERT: H 53 SER cc_start: 0.9453 (t) cc_final: 0.9155 (t) REVERT: H 54 LYS cc_start: 0.7961 (tppp) cc_final: 0.7747 (mmtp) REVERT: H 96 ARG cc_start: 0.8691 (ptm160) cc_final: 0.8346 (ttp-110) REVERT: L 1 MET cc_start: 0.3267 (ttp) cc_final: 0.2240 (tpp) REVERT: L 62 GLN cc_start: 0.7610 (tp40) cc_final: 0.7152 (tp40) REVERT: K 66 LYS cc_start: 0.8185 (mppt) cc_final: 0.7758 (pttt) REVERT: K 96 MET cc_start: -0.0645 (ttp) cc_final: -0.1349 (tpp) REVERT: K 147 MET cc_start: 0.4420 (mmt) cc_final: 0.3940 (mmt) REVERT: K 153 MET cc_start: 0.4071 (ppp) cc_final: 0.3846 (ppp) outliers start: 1 outliers final: 0 residues processed: 353 average time/residue: 0.3129 time to fit residues: 153.7206 Evaluate side-chains 297 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 297 time to evaluate : 1.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 10.0000 chunk 80 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 25 optimal weight: 0.3980 chunk 85 optimal weight: 10.0000 chunk 91 optimal weight: 6.9990 chunk 66 optimal weight: 0.9980 chunk 12 optimal weight: 9.9990 chunk 105 optimal weight: 30.0000 chunk 121 optimal weight: 3.9990 overall best weight: 2.2784 ------------------------------------------------------------------------------- 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 75 HIS B 93 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN D 79 HIS D 106 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS K 113 GLN K 181 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 1.2705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.059 16145 Z= 0.260 Angle : 0.724 10.447 23055 Z= 0.405 Chirality : 0.042 0.210 2607 Planarity : 0.005 0.046 1920 Dihedral : 31.739 145.467 4447 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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: -0.69 (0.24), residues: 1143 helix: 0.52 (0.19), residues: 686 sheet: -2.09 (0.70), residues: 55 loop : -1.89 (0.30), residues: 402 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 305 HIS 0.010 0.001 HIS G 31 PHE 0.027 0.003 PHE K 326 TYR 0.027 0.002 TYR F 51 ARG 0.008 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.250 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 45 THR cc_start: 0.8795 (m) cc_final: 0.8328 (m) REVERT: A 62 ILE cc_start: 0.9301 (tt) cc_final: 0.9090 (tt) REVERT: A 93 GLN cc_start: 0.8868 (tt0) cc_final: 0.8613 (tt0) REVERT: A 100 LEU cc_start: 0.9082 (mt) cc_final: 0.8789 (mp) REVERT: A 120 MET cc_start: 0.8676 (mmm) cc_final: 0.8358 (mmm) REVERT: B 52 GLU cc_start: 0.8741 (mp0) cc_final: 0.8414 (pm20) REVERT: B 74 GLU cc_start: 0.8612 (mm-30) cc_final: 0.8311 (mt-10) REVERT: C 25 PHE cc_start: 0.8257 (m-10) cc_final: 0.7987 (m-10) REVERT: C 36 LYS cc_start: 0.9409 (mmtt) cc_final: 0.9120 (mmmt) REVERT: C 73 ASN cc_start: 0.9044 (m-40) cc_final: 0.8787 (m-40) REVERT: C 91 GLU cc_start: 0.8151 (tm-30) cc_final: 0.7818 (tp30) REVERT: C 95 LYS cc_start: 0.9470 (tptp) cc_final: 0.9065 (tppt) REVERT: D 54 LYS cc_start: 0.8005 (ptmt) cc_final: 0.7241 (tttp) REVERT: D 58 ILE cc_start: 0.9168 (mm) cc_final: 0.8776 (mm) REVERT: D 65 ASP cc_start: 0.8898 (t70) cc_final: 0.8679 (t70) REVERT: D 82 LYS cc_start: 0.9511 (ttpt) cc_final: 0.8941 (mmtt) REVERT: D 83 ARG cc_start: 0.8968 (mmp80) cc_final: 0.8569 (mmp80) REVERT: D 93 THR cc_start: 0.8998 (p) cc_final: 0.8784 (p) REVERT: D 106 HIS cc_start: 0.8020 (m90) cc_final: 0.7626 (m90) REVERT: D 118 TYR cc_start: 0.9033 (t80) cc_final: 0.8630 (t80) REVERT: E 73 GLU cc_start: 0.7390 (pm20) cc_final: 0.7007 (pm20) REVERT: E 97 GLU cc_start: 0.8392 (tp30) cc_final: 0.7909 (tp30) REVERT: E 103 LEU cc_start: 0.9379 (tp) cc_final: 0.9170 (tp) REVERT: E 125 GLN cc_start: 0.9010 (pt0) cc_final: 0.8739 (pt0) REVERT: F 25 ASN cc_start: 0.6233 (m110) cc_final: 0.5865 (m110) REVERT: F 84 MET cc_start: 0.9035 (mmp) cc_final: 0.8450 (mmm) REVERT: G 57 TYR cc_start: 0.8790 (t80) cc_final: 0.8395 (t80) REVERT: G 71 ARG cc_start: 0.8609 (mmp80) cc_final: 0.8277 (mmp80) REVERT: G 76 THR cc_start: 0.9271 (p) cc_final: 0.9061 (t) REVERT: G 84 GLN cc_start: 0.9022 (tp40) cc_final: 0.8673 (tp40) REVERT: G 95 LYS cc_start: 0.8842 (tppp) cc_final: 0.8518 (tppp) REVERT: G 101 THR cc_start: 0.8817 (m) cc_final: 0.8513 (t) REVERT: H 43 LYS cc_start: 0.7423 (mttt) cc_final: 0.7149 (mttt) REVERT: H 51 ILE cc_start: 0.8532 (mt) cc_final: 0.8286 (mt) REVERT: H 53 SER cc_start: 0.9368 (t) cc_final: 0.9154 (t) REVERT: L 1 MET cc_start: 0.3385 (ttp) cc_final: 0.2481 (tpp) REVERT: L 62 GLN cc_start: 0.7627 (tp40) cc_final: 0.7152 (tp40) REVERT: K 66 LYS cc_start: 0.8167 (mppt) cc_final: 0.7740 (pttt) REVERT: K 96 MET cc_start: -0.0195 (ttp) cc_final: -0.1070 (tpp) REVERT: K 147 MET cc_start: 0.4922 (mmt) cc_final: 0.4582 (mmt) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.3184 time to fit residues: 160.2413 Evaluate side-chains 317 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 317 time to evaluate : 1.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 3.9990 chunk 117 optimal weight: 1.9990 chunk 124 optimal weight: 5.9990 chunk 75 optimal weight: 10.0000 chunk 54 optimal weight: 0.7980 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 0.6980 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 132 optimal weight: 9.9990 overall best weight: 2.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN A 125 GLN ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 112 GLN D 60 ASN D 79 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 46 HIS ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 109 HIS K 113 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 1.3445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 16145 Z= 0.298 Angle : 0.753 10.789 23055 Z= 0.420 Chirality : 0.042 0.200 2607 Planarity : 0.005 0.046 1920 Dihedral : 31.581 145.356 4447 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 22.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 0.00 % Allowed : 1.10 % Favored : 98.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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: -0.73 (0.24), residues: 1143 helix: 0.46 (0.19), residues: 685 sheet: -1.66 (0.80), residues: 49 loop : -1.93 (0.29), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 305 HIS 0.010 0.001 HIS D 79 PHE 0.023 0.002 PHE K 326 TYR 0.032 0.003 TYR D 80 ARG 0.010 0.001 ARG H 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 365 time to evaluate : 1.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.8967 (mt) cc_final: 0.8714 (mt) REVERT: A 62 ILE cc_start: 0.9264 (tt) cc_final: 0.8718 (tt) REVERT: A 100 LEU cc_start: 0.9089 (mt) cc_final: 0.8854 (mp) REVERT: A 125 GLN cc_start: 0.9054 (mp10) cc_final: 0.7857 (mm-40) REVERT: B 52 GLU cc_start: 0.8662 (mp0) cc_final: 0.8412 (pm20) REVERT: B 53 GLU cc_start: 0.8831 (mm-30) cc_final: 0.8329 (mm-30) REVERT: C 36 LYS cc_start: 0.9439 (mmtt) cc_final: 0.9155 (mmmt) REVERT: C 73 ASN cc_start: 0.9124 (m-40) cc_final: 0.8865 (m-40) REVERT: C 91 GLU cc_start: 0.8182 (tm-30) cc_final: 0.7956 (tp30) REVERT: C 95 LYS cc_start: 0.9498 (tptp) cc_final: 0.9074 (tppt) REVERT: D 54 LYS cc_start: 0.8074 (ptmt) cc_final: 0.7489 (tttp) REVERT: D 58 ILE cc_start: 0.9147 (mm) cc_final: 0.8873 (mm) REVERT: D 65 ASP cc_start: 0.8959 (t70) cc_final: 0.8737 (t70) REVERT: D 82 LYS cc_start: 0.9517 (ttpt) cc_final: 0.8917 (mmtt) REVERT: D 83 ARG cc_start: 0.9006 (mmp80) cc_final: 0.8559 (mmp80) REVERT: D 118 TYR cc_start: 0.9057 (t80) cc_final: 0.8590 (t80) REVERT: E 73 GLU cc_start: 0.7454 (pm20) cc_final: 0.6916 (pm20) REVERT: E 97 GLU cc_start: 0.8426 (tp30) cc_final: 0.7768 (tp30) REVERT: E 103 LEU cc_start: 0.9366 (tp) cc_final: 0.9163 (tp) REVERT: E 105 GLU cc_start: 0.8620 (tm-30) cc_final: 0.8047 (tm-30) REVERT: E 110 CYS cc_start: 0.9121 (m) cc_final: 0.8915 (m) REVERT: E 125 GLN cc_start: 0.9015 (pt0) cc_final: 0.8730 (pt0) REVERT: F 25 ASN cc_start: 0.6421 (m110) cc_final: 0.6088 (m110) REVERT: F 31 LYS cc_start: 0.8991 (tmtt) cc_final: 0.8569 (tptp) REVERT: F 37 LEU cc_start: 0.9579 (mm) cc_final: 0.9278 (mm) REVERT: F 59 LYS cc_start: 0.9307 (mmmt) cc_final: 0.9012 (mmmt) REVERT: F 75 HIS cc_start: 0.8660 (t70) cc_final: 0.8334 (t-170) REVERT: F 82 THR cc_start: 0.9268 (t) cc_final: 0.8642 (t) REVERT: F 84 MET cc_start: 0.9090 (mmp) cc_final: 0.8653 (mmm) REVERT: F 88 TYR cc_start: 0.9220 (m-10) cc_final: 0.8835 (m-80) REVERT: G 71 ARG cc_start: 0.8613 (mmp80) cc_final: 0.8306 (mmp80) REVERT: G 82 HIS cc_start: 0.8689 (m170) cc_final: 0.7841 (m90) REVERT: G 83 LEU cc_start: 0.8880 (mm) cc_final: 0.8640 (mm) REVERT: G 84 GLN cc_start: 0.8748 (tp-100) cc_final: 0.8444 (tp40) REVERT: G 92 GLU cc_start: 0.8561 (tp30) cc_final: 0.8217 (tp30) REVERT: G 101 THR cc_start: 0.8693 (m) cc_final: 0.8427 (p) REVERT: H 42 LEU cc_start: 0.8214 (tp) cc_final: 0.7835 (tp) REVERT: H 43 LYS cc_start: 0.7493 (mttt) cc_final: 0.7250 (mttm) REVERT: H 53 SER cc_start: 0.9436 (t) cc_final: 0.9175 (t) REVERT: H 106 HIS cc_start: 0.8875 (m90) cc_final: 0.8310 (m170) REVERT: L 1 MET cc_start: 0.3500 (ttp) cc_final: 0.2545 (tpp) REVERT: L 62 GLN cc_start: 0.7619 (tp40) cc_final: 0.7136 (tp40) REVERT: K 66 LYS cc_start: 0.8124 (mppt) cc_final: 0.7710 (pttt) REVERT: K 96 MET cc_start: -0.0562 (ttp) cc_final: -0.1380 (tpp) REVERT: K 147 MET cc_start: 0.4273 (mmt) cc_final: 0.3730 (mmt) REVERT: K 153 MET cc_start: 0.4144 (ppp) cc_final: 0.3567 (ppp) outliers start: 0 outliers final: 0 residues processed: 365 average time/residue: 0.3128 time to fit residues: 157.8426 Evaluate side-chains 327 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 327 time to evaluate : 1.167 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 5.9990 chunk 62 optimal weight: 8.9990 chunk 91 optimal weight: 8.9990 chunk 138 optimal weight: 4.9990 chunk 127 optimal weight: 20.0000 chunk 110 optimal weight: 10.0000 chunk 11 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 67 optimal weight: 0.9990 chunk 87 optimal weight: 10.0000 chunk 117 optimal weight: 6.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 104 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 60 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN D 79 HIS E 76 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 31 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 1.4634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.093 16145 Z= 0.385 Angle : 0.823 10.635 23055 Z= 0.455 Chirality : 0.045 0.299 2607 Planarity : 0.006 0.082 1920 Dihedral : 31.679 145.171 4447 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 26.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.30 % Favored : 93.70 % Rotamer: Outliers : 0.00 % Allowed : 0.70 % Favored : 99.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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: -0.99 (0.24), residues: 1143 helix: 0.15 (0.19), residues: 682 sheet: -1.87 (0.80), residues: 49 loop : -1.79 (0.29), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 205 HIS 0.006 0.001 HIS B 75 PHE 0.041 0.003 PHE E 67 TYR 0.072 0.004 TYR D 80 ARG 0.014 0.001 ARG C 77 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 363 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 363 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 LYS cc_start: 0.8112 (tttm) cc_final: 0.7821 (mtpp) REVERT: A 125 GLN cc_start: 0.8992 (mp10) cc_final: 0.8481 (mm-40) REVERT: B 52 GLU cc_start: 0.8692 (mp0) cc_final: 0.8397 (mp0) REVERT: B 53 GLU cc_start: 0.8815 (mm-30) cc_final: 0.8276 (mm-30) REVERT: B 88 TYR cc_start: 0.8374 (m-80) cc_final: 0.7951 (m-80) REVERT: C 36 LYS cc_start: 0.9473 (mmtt) cc_final: 0.9210 (mmmt) REVERT: C 91 GLU cc_start: 0.8300 (tm-30) cc_final: 0.8043 (tp30) REVERT: C 95 LYS cc_start: 0.9469 (tptp) cc_final: 0.9080 (tppt) REVERT: D 65 ASP cc_start: 0.9002 (t70) cc_final: 0.8687 (t0) REVERT: D 82 LYS cc_start: 0.9506 (ttpt) cc_final: 0.8998 (mmtt) REVERT: D 103 LEU cc_start: 0.9419 (tp) cc_final: 0.9217 (tp) REVERT: D 118 TYR cc_start: 0.9058 (t80) cc_final: 0.8485 (t80) REVERT: E 54 TYR cc_start: 0.7799 (m-80) cc_final: 0.7597 (m-80) REVERT: E 73 GLU cc_start: 0.7155 (pm20) cc_final: 0.6534 (pm20) REVERT: E 97 GLU cc_start: 0.8584 (tp30) cc_final: 0.7800 (tp30) REVERT: E 125 GLN cc_start: 0.8894 (pt0) cc_final: 0.8643 (pt0) REVERT: F 25 ASN cc_start: 0.6652 (m110) cc_final: 0.6139 (m110) REVERT: F 31 LYS cc_start: 0.9022 (tmtt) cc_final: 0.8668 (tptp) REVERT: F 45 ARG cc_start: 0.8583 (ttt180) cc_final: 0.7517 (mtp85) REVERT: F 51 TYR cc_start: 0.8693 (m-80) cc_final: 0.8243 (m-80) REVERT: F 70 VAL cc_start: 0.9803 (m) cc_final: 0.9442 (p) REVERT: F 82 THR cc_start: 0.9239 (t) cc_final: 0.8759 (t) REVERT: F 84 MET cc_start: 0.9079 (mmp) cc_final: 0.8505 (mmm) REVERT: F 88 TYR cc_start: 0.9265 (m-10) cc_final: 0.8885 (m-80) REVERT: F 92 ARG cc_start: 0.8366 (ttp-110) cc_final: 0.8098 (ttp80) REVERT: G 71 ARG cc_start: 0.8600 (mmp80) cc_final: 0.8276 (mmp80) REVERT: G 101 THR cc_start: 0.8718 (m) cc_final: 0.8412 (p) REVERT: H 42 LEU cc_start: 0.8294 (tp) cc_final: 0.7898 (tp) REVERT: H 43 LYS cc_start: 0.7711 (mttt) cc_final: 0.7452 (mttm) REVERT: H 106 HIS cc_start: 0.8852 (m90) cc_final: 0.8562 (m170) REVERT: L 1 MET cc_start: 0.3370 (ttp) cc_final: 0.2626 (tpp) REVERT: K 66 LYS cc_start: 0.8106 (mppt) cc_final: 0.7759 (pttt) REVERT: K 96 MET cc_start: -0.0385 (ttp) cc_final: -0.1376 (tpp) REVERT: K 153 MET cc_start: 0.4141 (ppp) cc_final: 0.3471 (ppp) outliers start: 0 outliers final: 0 residues processed: 363 average time/residue: 0.3102 time to fit residues: 156.7064 Evaluate side-chains 313 residues out of total 998 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 313 time to evaluate : 1.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.7980 chunk 101 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 0.0970 chunk 46 optimal weight: 0.3980 chunk 113 optimal weight: 8.9990 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 96 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN ** H 81 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 113 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4142 r_free = 0.4142 target = 0.130439 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.099361 restraints weight = 49720.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.101898 restraints weight = 26729.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.103440 restraints weight = 18319.934| |-----------------------------------------------------------------------------| r_work (final): 0.3642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7728 moved from start: 1.4723 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 16145 Z= 0.213 Angle : 0.705 12.917 23055 Z= 0.394 Chirality : 0.042 0.210 2607 Planarity : 0.005 0.050 1920 Dihedral : 31.495 144.593 4447 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 18.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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: -0.60 (0.24), residues: 1143 helix: 0.50 (0.19), residues: 683 sheet: -1.55 (0.82), residues: 49 loop : -1.73 (0.29), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 305 HIS 0.005 0.001 HIS B 75 PHE 0.027 0.002 PHE K 326 TYR 0.047 0.002 TYR D 80 ARG 0.018 0.001 ARG L 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3318.93 seconds wall clock time: 60 minutes 28.76 seconds (3628.76 seconds total)