Starting phenix.real_space_refine on Wed Feb 14 01:03:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/02_2024/8hik_34819_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/02_2024/8hik_34819.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/02_2024/8hik_34819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/02_2024/8hik_34819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/02_2024/8hik_34819_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/02_2024/8hik_34819_updated.pdb" } resolution = 3.72 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= 0.016 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 2 5.49 5 S 27 5.16 5 C 5296 2.51 5 N 1376 2.21 5 O 1537 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 15": "NH1" <-> "NH2" Residue "A ARG 26": "NH1" <-> "NH2" Residue "A ARG 91": "NH1" <-> "NH2" Residue "A ARG 157": "NH1" <-> "NH2" Residue "A ARG 303": "NH1" <-> "NH2" Residue "A ARG 373": "NH1" <-> "NH2" Residue "N ARG 27": "NH1" <-> "NH2" Residue "N TYR 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ARG 25": "NH1" <-> "NH2" Residue "L ARG 213": "NH1" <-> "NH2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 8238 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3969 Number of conformers: 1 Conformer: "" Number of residues, atoms: 498, 3969 Classifications: {'peptide': 498} Link IDs: {'PTRANS': 17, 'TRANS': 480} Chain breaks: 1 Chain: "H" Number of atoms: 1686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 225, 1686 Classifications: {'peptide': 225} Link IDs: {'PCIS': 2, 'PTRANS': 11, 'TRANS': 211} Chain: "N" Number of atoms: 925 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 925 Classifications: {'peptide': 120} Link IDs: {'PTRANS': 3, 'TRANS': 116} Chain: "L" Number of atoms: 1632 Number of conformers: 1 Conformer: "" Number of residues, atoms: 212, 1632 Classifications: {'peptide': 212} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 201} Chain: "A" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Unusual residues: {'TPP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.69, per 1000 atoms: 0.57 Number of scatterers: 8238 At special positions: 0 Unit cell: (66.34, 99.51, 148.73, 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 27 16.00 P 2 15.00 O 1537 8.00 N 1376 7.00 C 5296 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 154 " - pdb=" SG CYS H 210 " distance=2.03 Simple disulfide: pdb=" SG CYS N 22 " - pdb=" SG CYS N 96 " distance=2.03 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 136 " - pdb=" SG CYS L 196 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.06 Conformation dependent library (CDL) restraints added in 1.5 seconds 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1972 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 28 helices and 11 sheets defined 35.1% alpha, 17.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.56 Creating SS restraints... Processing helix chain 'A' and resid -79 through -64 removed outlier: 3.672A pdb=" N LYS A -64 " --> pdb=" O LYS A -68 " (cutoff:3.500A) Processing helix chain 'A' and resid -56 through -44 Processing helix chain 'A' and resid -37 through -34 No H-bonds generated for 'chain 'A' and resid -37 through -34' Processing helix chain 'A' and resid -24 through -4 removed outlier: 3.702A pdb=" N LEU A -5 " --> pdb=" O ASP A -9 " (cutoff:3.500A) Processing helix chain 'A' and resid 3 through 17 Processing helix chain 'A' and resid 19 through 22 Processing helix chain 'A' and resid 28 through 38 Processing helix chain 'A' and resid 48 through 52 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 69 through 80 Processing helix chain 'A' and resid 83 through 89 Processing helix chain 'A' and resid 93 through 111 Processing helix chain 'A' and resid 116 through 131 removed outlier: 4.145A pdb=" N VAL A 128 " --> pdb=" O LEU A 124 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N THR A 129 " --> pdb=" O PHE A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 134 through 143 Processing helix chain 'A' and resid 149 through 175 Processing helix chain 'A' and resid 182 through 201 Processing helix chain 'A' and resid 251 through 261 removed outlier: 4.323A pdb=" N ASP A 260 " --> pdb=" O ARG A 256 " (cutoff:3.500A) removed outlier: 4.649A pdb=" N SER A 261 " --> pdb=" O GLU A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 265 through 295 removed outlier: 3.936A pdb=" N TYR A 287 " --> pdb=" O LEU A 283 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 336 through 354 Processing helix chain 'A' and resid 362 through 374 Processing helix chain 'A' and resid 377 through 388 Proline residue: A 381 - end of helix removed outlier: 3.718A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 418 Processing helix chain 'A' and resid 428 through 450 Processing helix chain 'H' and resid 91 through 93 No H-bonds generated for 'chain 'H' and resid 91 through 93' Processing helix chain 'H' and resid 108 through 111 No H-bonds generated for 'chain 'H' and resid 108 through 111' Processing helix chain 'L' and resid 81 through 83 No H-bonds generated for 'chain 'L' and resid 81 through 83' Processing helix chain 'L' and resid 185 through 187 No H-bonds generated for 'chain 'L' and resid 185 through 187' Processing sheet with id= A, first strand: chain 'H' and resid 6 through 10 Processing sheet with id= B, first strand: chain 'H' and resid 121 through 123 removed outlier: 3.668A pdb=" N ALA H 52 " --> pdb=" O TRP H 39 " (cutoff:3.500A) removed outlier: 5.484A pdb=" N ARG H 41 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 5.065A pdb=" N TRP H 50 " --> pdb=" O ARG H 41 " (cutoff:3.500A) removed outlier: 7.245A pdb=" N ALA H 43 " --> pdb=" O LEU H 48 " (cutoff:3.500A) removed outlier: 6.437A pdb=" N LEU H 48 " --> pdb=" O ALA H 43 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'H' and resid 134 through 138 removed outlier: 6.145A pdb=" N TYR H 190 " --> pdb=" O ASP H 158 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'H' and resid 164 through 167 removed outlier: 4.332A pdb=" N TYR H 208 " --> pdb=" O VAL H 225 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'N' and resid 3 through 7 removed outlier: 3.735A pdb=" N SER N 7 " --> pdb=" O SER N 21 " (cutoff:3.500A) removed outlier: 4.160A pdb=" N SER N 21 " --> pdb=" O SER N 7 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'N' and resid 10 through 12 removed outlier: 3.833A pdb=" N THR N 118 " --> pdb=" O GLY N 10 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'N' and resid 92 through 98 removed outlier: 5.294A pdb=" N ARG N 38 " --> pdb=" O PHE N 47 " (cutoff:3.500A) removed outlier: 4.745A pdb=" N PHE N 47 " --> pdb=" O ARG N 38 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'L' and resid 20 through 25 Processing sheet with id= I, first strand: chain 'L' and resid 86 through 91 removed outlier: 6.366A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.870A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id= J, first strand: chain 'L' and resid 116 through 120 removed outlier: 5.961A pdb=" N TYR L 175 " --> pdb=" O ASN L 140 " (cutoff:3.500A) Processing sheet with id= K, first strand: chain 'L' and resid 194 through 198 368 hydrogen bonds defined for protein. 1059 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.17 Time building geometry restraints manager: 3.26 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2562 1.34 - 1.46: 2030 1.46 - 1.58: 3807 1.58 - 1.70: 3 1.70 - 1.81: 38 Bond restraints: 8440 Sorted by residual: bond pdb=" C5 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 1.727 1.510 0.217 1.00e-02 1.00e+04 4.69e+02 bond pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 1.675 1.544 0.131 1.00e-02 1.00e+04 1.71e+02 bond pdb=" C4' TPP A 601 " pdb=" N4' TPP A 601 " ideal model delta sigma weight residual 1.337 1.454 -0.117 1.10e-02 8.26e+03 1.13e+02 bond pdb=" C2 TPP A 601 " pdb=" N3 TPP A 601 " ideal model delta sigma weight residual 1.318 1.424 -0.106 1.30e-02 5.92e+03 6.66e+01 bond pdb=" O3A TPP A 601 " pdb=" PB TPP A 601 " ideal model delta sigma weight residual 1.587 1.662 -0.075 1.10e-02 8.26e+03 4.66e+01 ... (remaining 8435 not shown) Histogram of bond angle deviations from ideal: 99.98 - 106.78: 226 106.78 - 113.58: 4593 113.58 - 120.38: 3204 120.38 - 127.18: 3363 127.18 - 133.98: 98 Bond angle restraints: 11484 Sorted by residual: angle pdb=" PA TPP A 601 " pdb=" O3A TPP A 601 " pdb=" PB TPP A 601 " ideal model delta sigma weight residual 139.87 123.64 16.23 1.00e+00 1.00e+00 2.63e+02 angle pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " pdb=" C5 TPP A 601 " ideal model delta sigma weight residual 91.33 104.13 -12.80 1.00e+00 1.00e+00 1.64e+02 angle pdb=" C7 TPP A 601 " pdb=" O7 TPP A 601 " pdb=" PA TPP A 601 " ideal model delta sigma weight residual 124.29 118.57 5.72 1.00e+00 1.00e+00 3.27e+01 angle pdb=" N1' TPP A 601 " pdb=" C2' TPP A 601 " pdb=" N3' TPP A 601 " ideal model delta sigma weight residual 125.71 119.88 5.83 1.07e+00 8.80e-01 2.99e+01 angle pdb=" N3 TPP A 601 " pdb=" C2 TPP A 601 " pdb=" S1 TPP A 601 " ideal model delta sigma weight residual 112.34 107.32 5.02 1.00e+00 1.00e+00 2.52e+01 ... (remaining 11479 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4807 16.52 - 33.03: 110 33.03 - 49.54: 34 49.54 - 66.06: 1 66.06 - 82.57: 11 Dihedral angle restraints: 4963 sinusoidal: 1886 harmonic: 3077 Sorted by residual: dihedral pdb=" CB CYS H 154 " pdb=" SG CYS H 154 " pdb=" SG CYS H 210 " pdb=" CB CYS H 210 " ideal model delta sinusoidal sigma weight residual 93.00 175.57 -82.57 1 1.00e+01 1.00e-02 8.36e+01 dihedral pdb=" CB CYS L 136 " pdb=" SG CYS L 136 " pdb=" SG CYS L 196 " pdb=" CB CYS L 196 " ideal model delta sinusoidal sigma weight residual -86.00 -120.31 34.31 1 1.00e+01 1.00e-02 1.67e+01 dihedral pdb=" CA ARG A 91 " pdb=" C ARG A 91 " pdb=" N TYR A 92 " pdb=" CA TYR A 92 " ideal model delta harmonic sigma weight residual 180.00 159.67 20.33 0 5.00e+00 4.00e-02 1.65e+01 ... (remaining 4960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 957 0.049 - 0.097: 267 0.097 - 0.146: 64 0.146 - 0.195: 7 0.195 - 0.243: 1 Chirality restraints: 1296 Sorted by residual: chirality pdb=" CA THR A 69 " pdb=" N THR A 69 " pdb=" C THR A 69 " pdb=" CB THR A 69 " both_signs ideal model delta sigma weight residual False 2.53 2.28 0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CB THR A 69 " pdb=" CA THR A 69 " pdb=" OG1 THR A 69 " pdb=" CG2 THR A 69 " both_signs ideal model delta sigma weight residual False 2.55 2.36 0.19 2.00e-01 2.50e+01 9.13e-01 chirality pdb=" CA TYR N 104 " pdb=" N TYR N 104 " pdb=" C TYR N 104 " pdb=" CB TYR N 104 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.80e-01 ... (remaining 1293 not shown) Planarity restraints: 1437 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 102 " -0.016 2.00e-02 2.50e+03 1.51e-02 5.66e+00 pdb=" CG TRP H 102 " 0.041 2.00e-02 2.50e+03 pdb=" CD1 TRP H 102 " -0.018 2.00e-02 2.50e+03 pdb=" CD2 TRP H 102 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP H 102 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP H 102 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 102 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 102 " 0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 102 " -0.005 2.00e-02 2.50e+03 pdb=" CH2 TRP H 102 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TRP H 105 " 0.038 5.00e-02 4.00e+02 5.76e-02 5.31e+00 pdb=" N PRO H 106 " -0.100 5.00e-02 4.00e+02 pdb=" CA PRO H 106 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO H 106 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 108 " -0.035 5.00e-02 4.00e+02 5.18e-02 4.29e+00 pdb=" N PRO H 109 " 0.090 5.00e-02 4.00e+02 pdb=" CA PRO H 109 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO H 109 " -0.030 5.00e-02 4.00e+02 ... (remaining 1434 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 2248 2.81 - 3.33: 7166 3.33 - 3.85: 13560 3.85 - 4.38: 15172 4.38 - 4.90: 26558 Nonbonded interactions: 64704 Sorted by model distance: nonbonded pdb=" OG SER A 168 " pdb=" O GLY A 307 " model vdw 2.282 2.440 nonbonded pdb=" OG SER L 64 " pdb=" OG1 THR L 75 " model vdw 2.326 2.440 nonbonded pdb=" O GLU A -26 " pdb=" OH TYR A 22 " model vdw 2.336 2.440 nonbonded pdb=" NE ARG A -49 " pdb=" O LEU L 93 " model vdw 2.340 2.520 nonbonded pdb=" O TRP H 111 " pdb=" OH TYR L 92 " model vdw 2.345 2.440 ... (remaining 64699 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 2.750 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: 0.020 Extract box with map and model: 6.900 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.740 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6165 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 : 0.005 0.217 8440 Z= 0.342 Angle : 0.820 16.228 11484 Z= 0.473 Chirality : 0.047 0.243 1296 Planarity : 0.006 0.058 1437 Dihedral : 9.444 75.327 2976 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 4.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.26 % Favored : 94.74 % Rotamer: Outliers : 0.00 % Allowed : 1.23 % Favored : 98.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.54 (0.21), residues: 1045 helix: -1.96 (0.20), residues: 380 sheet: -1.92 (0.29), residues: 241 loop : -2.84 (0.25), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 102 HIS 0.006 0.002 HIS H 38 PHE 0.029 0.002 PHE A 103 TYR 0.023 0.002 TYR H 53 ARG 0.006 0.000 ARG L 62 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 217 time to evaluate : 0.925 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7460 (tttt) cc_final: 0.7258 (mtmm) REVERT: A -50 MET cc_start: 0.6245 (mmm) cc_final: 0.5921 (mmm) REVERT: A -22 PHE cc_start: 0.7319 (t80) cc_final: 0.6815 (t80) REVERT: A 27 HIS cc_start: 0.5170 (m90) cc_final: 0.4851 (m-70) REVERT: A 73 SER cc_start: 0.6585 (m) cc_final: 0.6352 (t) REVERT: A 140 ILE cc_start: 0.7951 (mt) cc_final: 0.7742 (tp) REVERT: A 281 TYR cc_start: 0.6510 (t80) cc_final: 0.6203 (t80) REVERT: A 304 VAL cc_start: 0.7185 (t) cc_final: 0.5916 (m) REVERT: A 386 GLN cc_start: 0.7578 (mm-40) cc_final: 0.7062 (tm-30) REVERT: A 387 ILE cc_start: 0.7155 (mt) cc_final: 0.6955 (mt) REVERT: H 86 MET cc_start: 0.6378 (mtm) cc_final: 0.6146 (mtm) REVERT: H 99 CYS cc_start: 0.5632 (t) cc_final: 0.5367 (t) REVERT: H 112 LYS cc_start: 0.7716 (mttt) cc_final: 0.7507 (ttmm) REVERT: H 119 GLN cc_start: 0.6958 (mt0) cc_final: 0.6698 (mt0) REVERT: H 135 VAL cc_start: 0.7872 (t) cc_final: 0.7591 (m) REVERT: H 136 PHE cc_start: 0.7525 (m-80) cc_final: 0.7085 (m-80) REVERT: N 34 MET cc_start: 0.6441 (mtp) cc_final: 0.6215 (mtp) REVERT: L 32 SER cc_start: 0.7747 (t) cc_final: 0.7452 (p) REVERT: L 37 TYR cc_start: 0.8263 (m-10) cc_final: 0.7688 (m-80) REVERT: L 43 LYS cc_start: 0.8431 (mttt) cc_final: 0.8094 (ttmm) outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1900 time to fit residues: 56.5301 Evaluate side-chains 184 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 184 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 87 optimal weight: 3.9990 chunk 78 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.6980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 94 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -77 ASN A -42 GLN A 27 HIS A 120 GLN A 289 HIS A 358 HIS A 431 GLN H 178 HIS H 214 HIS L 28 GLN L 90 GLN L 162 GLN L 191 HIS Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6512 moved from start: 0.2992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.098 8440 Z= 0.310 Angle : 0.644 8.170 11484 Z= 0.333 Chirality : 0.042 0.156 1296 Planarity : 0.005 0.050 1437 Dihedral : 5.338 43.293 1159 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 12.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.91 % Allowed : 9.18 % Favored : 87.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -2.27 (0.24), residues: 1045 helix: -0.41 (0.25), residues: 373 sheet: -1.54 (0.31), residues: 244 loop : -2.41 (0.28), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP H 102 HIS 0.006 0.002 HIS H 38 PHE 0.020 0.002 PHE L 211 TYR 0.032 0.002 TYR A 126 ARG 0.006 0.001 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 248 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 222 time to evaluate : 0.842 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -50 MET cc_start: 0.6604 (mmm) cc_final: 0.6355 (mmm) REVERT: A 27 HIS cc_start: 0.5619 (m-70) cc_final: 0.5147 (m-70) REVERT: A 73 SER cc_start: 0.7640 (m) cc_final: 0.7234 (t) REVERT: A 79 VAL cc_start: 0.7662 (m) cc_final: 0.7456 (t) REVERT: A 99 GLN cc_start: 0.7829 (tt0) cc_final: 0.7404 (tt0) REVERT: A 281 TYR cc_start: 0.6721 (t80) cc_final: 0.6285 (t80) REVERT: A 294 GLU cc_start: 0.6987 (tt0) cc_final: 0.6750 (tt0) REVERT: A 386 GLN cc_start: 0.7512 (mm-40) cc_final: 0.6980 (tm-30) REVERT: A 387 ILE cc_start: 0.7204 (mt) cc_final: 0.6877 (mt) REVERT: A 451 MET cc_start: 0.4835 (ttt) cc_final: 0.4619 (ttp) REVERT: H 46 LYS cc_start: 0.8422 (mmtt) cc_final: 0.8197 (mmmm) REVERT: H 53 TYR cc_start: 0.7915 (p90) cc_final: 0.7712 (p90) REVERT: H 63 TYR cc_start: 0.7626 (m-10) cc_final: 0.7188 (m-10) REVERT: H 86 MET cc_start: 0.6910 (mtm) cc_final: 0.6393 (mtm) REVERT: H 110 TRP cc_start: 0.8039 (t60) cc_final: 0.7023 (t60) REVERT: H 135 VAL cc_start: 0.7886 (t) cc_final: 0.7523 (m) REVERT: L 36 TRP cc_start: 0.8225 (m100) cc_final: 0.7973 (m100) REVERT: L 43 LYS cc_start: 0.8657 (mttt) cc_final: 0.8378 (mtpp) REVERT: L 47 LEU cc_start: 0.8620 (tp) cc_final: 0.8352 (tt) REVERT: L 137 LEU cc_start: 0.8128 (tp) cc_final: 0.7876 (tt) outliers start: 26 outliers final: 13 residues processed: 230 average time/residue: 0.1870 time to fit residues: 60.2695 Evaluate side-chains 211 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 198 time to evaluate : 0.838 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 290 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.5980 chunk 29 optimal weight: 0.0670 chunk 78 optimal weight: 0.6980 chunk 64 optimal weight: 0.4980 chunk 26 optimal weight: 0.8980 chunk 94 optimal weight: 0.7980 chunk 102 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 75 optimal weight: 0.8980 overall best weight: 0.4918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -20 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6538 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.064 8440 Z= 0.234 Angle : 0.595 7.626 11484 Z= 0.298 Chirality : 0.041 0.140 1296 Planarity : 0.004 0.048 1437 Dihedral : 5.042 38.564 1159 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.69 % Allowed : 13.10 % Favored : 84.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.71 (0.25), residues: 1045 helix: 0.13 (0.26), residues: 377 sheet: -1.28 (0.31), residues: 245 loop : -2.16 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 102 HIS 0.003 0.001 HIS H 38 PHE 0.017 0.001 PHE A 212 TYR 0.025 0.002 TYR A 126 ARG 0.004 0.001 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 202 time to evaluate : 0.918 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8195 (tttt) cc_final: 0.7939 (ttpt) REVERT: A -51 LYS cc_start: 0.7667 (tttt) cc_final: 0.7417 (mtmm) REVERT: A 67 GLU cc_start: 0.7817 (tt0) cc_final: 0.7508 (tt0) REVERT: A 73 SER cc_start: 0.7743 (m) cc_final: 0.7302 (t) REVERT: A 79 VAL cc_start: 0.7684 (m) cc_final: 0.7370 (t) REVERT: A 99 GLN cc_start: 0.7495 (tt0) cc_final: 0.7077 (tt0) REVERT: A 104 VAL cc_start: 0.7270 (t) cc_final: 0.7067 (p) REVERT: A 150 GLN cc_start: 0.7817 (mm-40) cc_final: 0.7582 (mm-40) REVERT: A 264 ARG cc_start: 0.4629 (ttp-110) cc_final: 0.4064 (mtp-110) REVERT: A 294 GLU cc_start: 0.6932 (tt0) cc_final: 0.6662 (tt0) REVERT: A 386 GLN cc_start: 0.7447 (mm-40) cc_final: 0.6915 (tm-30) REVERT: A 387 ILE cc_start: 0.7120 (mt) cc_final: 0.6868 (mt) REVERT: H 63 TYR cc_start: 0.7603 (m-10) cc_final: 0.7228 (m-10) REVERT: H 111 TRP cc_start: 0.7980 (m100) cc_final: 0.6754 (m100) REVERT: H 135 VAL cc_start: 0.7869 (t) cc_final: 0.7594 (m) REVERT: L 36 TRP cc_start: 0.8184 (m100) cc_final: 0.7964 (m100) REVERT: L 43 LYS cc_start: 0.8681 (mttt) cc_final: 0.8386 (mtpp) REVERT: L 87 TYR cc_start: 0.8686 (m-80) cc_final: 0.8182 (m-10) outliers start: 24 outliers final: 16 residues processed: 210 average time/residue: 0.1865 time to fit residues: 54.6901 Evaluate side-chains 211 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 195 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain A residue 434 LEU Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 75 THR Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.7980 chunk 71 optimal weight: 0.9980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 0.0370 chunk 45 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 94 optimal weight: 0.9990 chunk 100 optimal weight: 0.9990 chunk 89 optimal weight: 0.0370 chunk 27 optimal weight: 0.5980 chunk 83 optimal weight: 0.8980 overall best weight: 0.4736 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 277 ASN H 169 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6576 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 8440 Z= 0.229 Angle : 0.584 8.248 11484 Z= 0.295 Chirality : 0.041 0.158 1296 Planarity : 0.004 0.050 1437 Dihedral : 4.880 29.953 1159 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 3.14 % Allowed : 14.67 % Favored : 82.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.26), residues: 1045 helix: 0.39 (0.26), residues: 377 sheet: -1.03 (0.32), residues: 246 loop : -1.88 (0.31), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP H 102 HIS 0.005 0.001 HIS A -20 PHE 0.016 0.001 PHE H 114 TYR 0.022 0.002 TYR A 126 ARG 0.004 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 235 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 207 time to evaluate : 0.936 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8217 (tttt) cc_final: 0.7904 (ttpt) REVERT: A -51 LYS cc_start: 0.7579 (tttt) cc_final: 0.7282 (mtmm) REVERT: A -49 ARG cc_start: 0.7711 (tpt-90) cc_final: 0.7178 (ttm170) REVERT: A 53 LEU cc_start: 0.6095 (mp) cc_final: 0.5834 (mt) REVERT: A 73 SER cc_start: 0.7949 (m) cc_final: 0.7496 (t) REVERT: A 79 VAL cc_start: 0.7809 (m) cc_final: 0.7517 (t) REVERT: A 99 GLN cc_start: 0.7535 (tt0) cc_final: 0.7196 (tt0) REVERT: A 264 ARG cc_start: 0.4700 (ttp-110) cc_final: 0.4364 (mtm110) REVERT: A 294 GLU cc_start: 0.6942 (tt0) cc_final: 0.6684 (tt0) REVERT: A 386 GLN cc_start: 0.7370 (mm-40) cc_final: 0.6936 (tt0) REVERT: A 387 ILE cc_start: 0.7087 (mt) cc_final: 0.6869 (mt) REVERT: H 20 SER cc_start: 0.8126 (m) cc_final: 0.7770 (p) REVERT: H 63 TYR cc_start: 0.7696 (m-10) cc_final: 0.7318 (m-10) REVERT: H 135 VAL cc_start: 0.7895 (t) cc_final: 0.7650 (m) REVERT: H 155 LEU cc_start: 0.7501 (tp) cc_final: 0.7282 (tt) REVERT: N 34 MET cc_start: 0.6282 (mtt) cc_final: 0.6055 (mtt) REVERT: L 48 LEU cc_start: 0.7912 (tp) cc_final: 0.7449 (tp) REVERT: L 94 TYR cc_start: 0.7580 (t80) cc_final: 0.7320 (t80) REVERT: L 166 THR cc_start: 0.8622 (t) cc_final: 0.8230 (m) outliers start: 28 outliers final: 17 residues processed: 219 average time/residue: 0.1969 time to fit residues: 59.0291 Evaluate side-chains 212 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 195 time to evaluate : 0.868 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 21 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 53 SER Chi-restraints excluded: chain L residue 89 CYS Chi-restraints excluded: chain L residue 97 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 57 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 74 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 85 optimal weight: 0.9990 chunk 69 optimal weight: 0.0020 chunk 0 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 90 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.3980 overall best weight: 0.5188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6603 moved from start: 0.4653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 8440 Z= 0.240 Angle : 0.599 9.071 11484 Z= 0.301 Chirality : 0.041 0.134 1296 Planarity : 0.004 0.049 1437 Dihedral : 4.824 24.965 1159 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 13.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 2.69 % Allowed : 16.35 % Favored : 80.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.25 (0.26), residues: 1045 helix: 0.38 (0.26), residues: 382 sheet: -0.91 (0.33), residues: 246 loop : -1.87 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 102 HIS 0.004 0.001 HIS A -20 PHE 0.012 0.001 PHE A 103 TYR 0.022 0.002 TYR A 126 ARG 0.005 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 198 time to evaluate : 0.906 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8302 (tttt) cc_final: 0.8094 (ttpt) REVERT: A -51 LYS cc_start: 0.7608 (tttt) cc_final: 0.7308 (mtmm) REVERT: A 53 LEU cc_start: 0.6164 (mp) cc_final: 0.5947 (mt) REVERT: A 73 SER cc_start: 0.7898 (m) cc_final: 0.7452 (t) REVERT: A 79 VAL cc_start: 0.7820 (m) cc_final: 0.7475 (t) REVERT: A 80 LEU cc_start: 0.8230 (tp) cc_final: 0.7921 (tt) REVERT: A 99 GLN cc_start: 0.7619 (tt0) cc_final: 0.7062 (tt0) REVERT: A 122 MET cc_start: 0.7269 (tmm) cc_final: 0.5968 (tmm) REVERT: A 386 GLN cc_start: 0.7347 (mm-40) cc_final: 0.6892 (tt0) REVERT: A 387 ILE cc_start: 0.7118 (mt) cc_final: 0.6896 (mt) REVERT: H 20 SER cc_start: 0.8156 (m) cc_final: 0.7779 (p) REVERT: H 63 TYR cc_start: 0.7718 (m-10) cc_final: 0.7263 (m-10) REVERT: H 110 TRP cc_start: 0.8322 (t60) cc_final: 0.7074 (t60) REVERT: H 135 VAL cc_start: 0.7910 (t) cc_final: 0.7665 (m) REVERT: N 34 MET cc_start: 0.6367 (mtt) cc_final: 0.6141 (mtt) REVERT: L 36 TRP cc_start: 0.8244 (m100) cc_final: 0.7975 (m100) REVERT: L 48 LEU cc_start: 0.7785 (tp) cc_final: 0.7457 (tp) REVERT: L 87 TYR cc_start: 0.8679 (m-80) cc_final: 0.8229 (m-10) REVERT: L 92 TYR cc_start: 0.8156 (p90) cc_final: 0.7780 (p90) REVERT: L 166 THR cc_start: 0.8617 (t) cc_final: 0.8189 (m) outliers start: 24 outliers final: 15 residues processed: 207 average time/residue: 0.2041 time to fit residues: 57.3426 Evaluate side-chains 217 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 0.921 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 90 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 59 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 100 optimal weight: 0.8980 chunk 83 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 52 optimal weight: 0.8980 chunk 97 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** N 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 4 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.070 8440 Z= 0.283 Angle : 0.627 7.945 11484 Z= 0.318 Chirality : 0.042 0.136 1296 Planarity : 0.004 0.050 1437 Dihedral : 4.960 22.903 1159 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 3.02 % Allowed : 16.91 % Favored : 80.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.26), residues: 1045 helix: 0.22 (0.26), residues: 382 sheet: -0.78 (0.33), residues: 238 loop : -1.85 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 168 HIS 0.004 0.001 HIS A 27 PHE 0.013 0.001 PHE A 103 TYR 0.027 0.002 TYR A 126 ARG 0.005 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 201 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8301 (tttt) cc_final: 0.8030 (ttpt) REVERT: A -51 LYS cc_start: 0.7750 (tttt) cc_final: 0.7508 (mtmm) REVERT: A 2 LYS cc_start: 0.7774 (ptpt) cc_final: 0.7541 (ptpt) REVERT: A 53 LEU cc_start: 0.6348 (mp) cc_final: 0.5931 (mt) REVERT: A 73 SER cc_start: 0.8026 (m) cc_final: 0.7576 (t) REVERT: A 80 LEU cc_start: 0.8341 (tp) cc_final: 0.8023 (tt) REVERT: A 99 GLN cc_start: 0.7603 (tt0) cc_final: 0.7057 (tt0) REVERT: A 122 MET cc_start: 0.7158 (tmm) cc_final: 0.5984 (tmm) REVERT: A 165 PHE cc_start: 0.7708 (t80) cc_final: 0.7277 (t80) REVERT: A 170 LEU cc_start: 0.7211 (tp) cc_final: 0.6935 (tt) REVERT: A 386 GLN cc_start: 0.7320 (mm-40) cc_final: 0.6909 (tt0) REVERT: A 387 ILE cc_start: 0.7135 (mt) cc_final: 0.6889 (mt) REVERT: A 440 LEU cc_start: 0.5768 (tp) cc_final: 0.5563 (tt) REVERT: H 20 SER cc_start: 0.8237 (m) cc_final: 0.7906 (p) REVERT: H 63 TYR cc_start: 0.7676 (m-10) cc_final: 0.7211 (m-10) REVERT: H 110 TRP cc_start: 0.8414 (t60) cc_final: 0.7114 (t60) REVERT: N 34 MET cc_start: 0.6376 (mtt) cc_final: 0.6125 (mtt) REVERT: L 7 GLN cc_start: 0.7303 (tt0) cc_final: 0.6955 (tt0) REVERT: L 32 SER cc_start: 0.8208 (t) cc_final: 0.7976 (p) REVERT: L 36 TRP cc_start: 0.8262 (m100) cc_final: 0.7922 (m100) REVERT: L 48 LEU cc_start: 0.7764 (tp) cc_final: 0.7419 (tp) REVERT: L 87 TYR cc_start: 0.8585 (m-80) cc_final: 0.8285 (m-10) REVERT: L 92 TYR cc_start: 0.8176 (p90) cc_final: 0.7838 (p90) REVERT: L 166 THR cc_start: 0.8610 (t) cc_final: 0.8148 (m) outliers start: 27 outliers final: 23 residues processed: 211 average time/residue: 0.1988 time to fit residues: 57.4928 Evaluate side-chains 221 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 198 time to evaluate : 0.872 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain A residue 345 THR Chi-restraints excluded: chain A residue 375 SER Chi-restraints excluded: chain A residue 412 THR Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain N residue 20 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 73 optimal weight: 1.9990 chunk 56 optimal weight: 0.7980 chunk 84 optimal weight: 0.8980 chunk 100 optimal weight: 0.9980 chunk 62 optimal weight: 0.9990 chunk 61 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 59 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.5535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 8440 Z= 0.303 Angle : 0.640 8.995 11484 Z= 0.326 Chirality : 0.043 0.162 1296 Planarity : 0.004 0.049 1437 Dihedral : 5.021 24.629 1159 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 15.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.91 % Allowed : 17.92 % Favored : 79.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.26), residues: 1045 helix: 0.21 (0.26), residues: 381 sheet: -0.77 (0.33), residues: 238 loop : -1.83 (0.31), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 168 HIS 0.004 0.001 HIS A -20 PHE 0.015 0.001 PHE N 68 TYR 0.026 0.002 TYR A 126 ARG 0.006 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 203 time to evaluate : 0.931 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A -56 LYS cc_start: 0.8340 (tttt) cc_final: 0.8106 (ttpt) REVERT: A -51 LYS cc_start: 0.7883 (tttt) cc_final: 0.7499 (mtmm) REVERT: A -50 MET cc_start: 0.6768 (OUTLIER) cc_final: 0.6422 (tmm) REVERT: A -49 ARG cc_start: 0.7681 (tpt-90) cc_final: 0.7225 (tpp80) REVERT: A 3 GLU cc_start: 0.7203 (mm-30) cc_final: 0.6949 (mm-30) REVERT: A 53 LEU cc_start: 0.6384 (mp) cc_final: 0.5940 (mt) REVERT: A 73 SER cc_start: 0.8057 (m) cc_final: 0.7691 (t) REVERT: A 99 GLN cc_start: 0.7664 (tt0) cc_final: 0.7146 (tt0) REVERT: A 165 PHE cc_start: 0.7720 (t80) cc_final: 0.7129 (t80) REVERT: A 170 LEU cc_start: 0.7134 (tp) cc_final: 0.6887 (tt) REVERT: A 294 GLU cc_start: 0.6995 (tt0) cc_final: 0.6739 (tt0) REVERT: A 366 TYR cc_start: 0.7109 (m-80) cc_final: 0.6826 (m-80) REVERT: A 386 GLN cc_start: 0.7220 (mm-40) cc_final: 0.7015 (tp40) REVERT: A 387 ILE cc_start: 0.7110 (mt) cc_final: 0.6867 (mt) REVERT: H 20 SER cc_start: 0.8285 (m) cc_final: 0.7956 (p) REVERT: H 63 TYR cc_start: 0.7711 (m-10) cc_final: 0.7256 (m-10) REVERT: H 110 TRP cc_start: 0.8428 (t60) cc_final: 0.7123 (t60) REVERT: H 136 PHE cc_start: 0.7521 (m-80) cc_final: 0.7166 (m-80) REVERT: N 34 MET cc_start: 0.6296 (mtt) cc_final: 0.6041 (mtt) REVERT: L 7 GLN cc_start: 0.7355 (tt0) cc_final: 0.7032 (tt0) REVERT: L 32 SER cc_start: 0.8247 (t) cc_final: 0.8037 (p) REVERT: L 36 TRP cc_start: 0.8279 (m100) cc_final: 0.7940 (m100) REVERT: L 48 LEU cc_start: 0.7761 (tp) cc_final: 0.7440 (tp) REVERT: L 87 TYR cc_start: 0.8610 (m-80) cc_final: 0.8329 (m-10) REVERT: L 92 TYR cc_start: 0.8203 (p90) cc_final: 0.7822 (p90) REVERT: L 166 THR cc_start: 0.8596 (t) cc_final: 0.8146 (m) outliers start: 26 outliers final: 21 residues processed: 213 average time/residue: 0.1984 time to fit residues: 58.3471 Evaluate side-chains 221 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 199 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 49 THR Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 310 ASP Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 174 THR Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 200 SER Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 83 ASP Chi-restraints excluded: chain L residue 89 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 30 optimal weight: 4.9990 chunk 19 optimal weight: 0.7980 chunk 63 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 49 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 78 optimal weight: 0.5980 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.6980 chunk 87 optimal weight: 0.1980 chunk 93 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.5624 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 8440 Z= 0.246 Angle : 0.625 9.967 11484 Z= 0.311 Chirality : 0.041 0.143 1296 Planarity : 0.004 0.051 1437 Dihedral : 4.938 25.825 1159 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 14.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.69 % Allowed : 18.81 % Favored : 78.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.11 (0.26), residues: 1045 helix: 0.31 (0.25), residues: 383 sheet: -0.73 (0.33), residues: 245 loop : -1.65 (0.31), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 168 HIS 0.003 0.001 HIS A 355 PHE 0.017 0.001 PHE A 103 TYR 0.028 0.002 TYR A 92 ARG 0.005 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 197 time to evaluate : 0.748 Fit side-chains revert: symmetry clash REVERT: A -76 TRP cc_start: 0.6332 (t-100) cc_final: 0.5655 (t-100) REVERT: A -51 LYS cc_start: 0.7861 (tttt) cc_final: 0.7441 (mtmm) REVERT: A -50 MET cc_start: 0.6722 (OUTLIER) cc_final: 0.6446 (tmm) REVERT: A -49 ARG cc_start: 0.7655 (tpt-90) cc_final: 0.7224 (tpp80) REVERT: A 2 LYS cc_start: 0.7847 (ptpt) cc_final: 0.6524 (tptp) REVERT: A 3 GLU cc_start: 0.7148 (mm-30) cc_final: 0.6783 (mm-30) REVERT: A 53 LEU cc_start: 0.6352 (mp) cc_final: 0.5883 (mt) REVERT: A 72 LEU cc_start: 0.7268 (tp) cc_final: 0.6739 (tp) REVERT: A 99 GLN cc_start: 0.7567 (tt0) cc_final: 0.7053 (tt0) REVERT: A 123 GLU cc_start: 0.6720 (mm-30) cc_final: 0.6358 (mm-30) REVERT: A 148 ARG cc_start: 0.7301 (OUTLIER) cc_final: 0.6429 (mtt90) REVERT: A 165 PHE cc_start: 0.7710 (t80) cc_final: 0.7465 (t80) REVERT: A 264 ARG cc_start: 0.4127 (mtm110) cc_final: 0.3915 (mtm110) REVERT: A 366 TYR cc_start: 0.7093 (m-80) cc_final: 0.6837 (m-80) REVERT: A 386 GLN cc_start: 0.7313 (mm-40) cc_final: 0.7106 (tp40) REVERT: A 387 ILE cc_start: 0.7117 (mt) cc_final: 0.6875 (mt) REVERT: H 20 SER cc_start: 0.8315 (m) cc_final: 0.7962 (p) REVERT: H 63 TYR cc_start: 0.7701 (m-10) cc_final: 0.7313 (m-10) REVERT: H 110 TRP cc_start: 0.8409 (t60) cc_final: 0.7036 (t60) REVERT: H 136 PHE cc_start: 0.7481 (m-80) cc_final: 0.7166 (m-80) REVERT: N 34 MET cc_start: 0.6315 (mtt) cc_final: 0.6067 (mtt) REVERT: L 32 SER cc_start: 0.8170 (t) cc_final: 0.7891 (p) REVERT: L 36 TRP cc_start: 0.8227 (m100) cc_final: 0.7908 (m100) REVERT: L 87 TYR cc_start: 0.8628 (m-80) cc_final: 0.8371 (m-10) REVERT: L 92 TYR cc_start: 0.8183 (p90) cc_final: 0.7683 (p90) outliers start: 24 outliers final: 17 residues processed: 207 average time/residue: 0.2162 time to fit residues: 61.2381 Evaluate side-chains 216 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 197 time to evaluate : 0.875 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 130 MET Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 53 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 40 optimal weight: 0.3980 chunk 73 optimal weight: 2.9990 chunk 28 optimal weight: 0.1980 chunk 84 optimal weight: 0.3980 chunk 88 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 1.9990 chunk 60 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 HIS A 150 GLN ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6652 moved from start: 0.5730 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 8440 Z= 0.254 Angle : 0.665 13.005 11484 Z= 0.326 Chirality : 0.041 0.145 1296 Planarity : 0.004 0.049 1437 Dihedral : 4.982 26.459 1159 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.69 % Allowed : 19.26 % Favored : 78.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.26), residues: 1045 helix: 0.31 (0.25), residues: 381 sheet: -0.73 (0.33), residues: 250 loop : -1.57 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP H 168 HIS 0.002 0.001 HIS A 355 PHE 0.016 0.001 PHE A -22 TYR 0.037 0.002 TYR A 92 ARG 0.005 0.000 ARG N 52 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 207 time to evaluate : 0.869 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7853 (tttt) cc_final: 0.7438 (mtmm) REVERT: A -50 MET cc_start: 0.6650 (OUTLIER) cc_final: 0.6122 (tmm) REVERT: A -49 ARG cc_start: 0.7612 (tpt-90) cc_final: 0.7080 (tpp80) REVERT: A 53 LEU cc_start: 0.6383 (mp) cc_final: 0.6161 (mt) REVERT: A 72 LEU cc_start: 0.7159 (tp) cc_final: 0.6618 (tp) REVERT: A 99 GLN cc_start: 0.7631 (tt0) cc_final: 0.7081 (tt0) REVERT: A 123 GLU cc_start: 0.6782 (mm-30) cc_final: 0.6399 (mm-30) REVERT: A 148 ARG cc_start: 0.7241 (OUTLIER) cc_final: 0.6437 (mtt90) REVERT: A 165 PHE cc_start: 0.7722 (t80) cc_final: 0.7116 (t80) REVERT: A 386 GLN cc_start: 0.7225 (mm-40) cc_final: 0.7019 (tp40) REVERT: A 387 ILE cc_start: 0.7112 (mt) cc_final: 0.6880 (mt) REVERT: H 20 SER cc_start: 0.8326 (m) cc_final: 0.8006 (p) REVERT: H 63 TYR cc_start: 0.7724 (m-10) cc_final: 0.7370 (m-10) REVERT: H 110 TRP cc_start: 0.8401 (t60) cc_final: 0.6967 (t60) REVERT: H 136 PHE cc_start: 0.7505 (m-80) cc_final: 0.7243 (m-80) REVERT: H 180 PHE cc_start: 0.8326 (m-80) cc_final: 0.8099 (m-80) REVERT: N 34 MET cc_start: 0.6304 (mtt) cc_final: 0.6086 (mtt) REVERT: N 83 MET cc_start: 0.6773 (ptm) cc_final: 0.6418 (ttp) REVERT: N 86 LEU cc_start: 0.7406 (tp) cc_final: 0.7178 (tp) REVERT: L 32 SER cc_start: 0.8234 (t) cc_final: 0.7925 (p) REVERT: L 92 TYR cc_start: 0.8074 (p90) cc_final: 0.7764 (p90) REVERT: L 94 TYR cc_start: 0.7727 (t80) cc_final: 0.7450 (t80) outliers start: 24 outliers final: 20 residues processed: 216 average time/residue: 0.1982 time to fit residues: 58.5063 Evaluate side-chains 219 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 197 time to evaluate : 0.870 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain A residue 207 LYS Chi-restraints excluded: chain H residue 61 THR Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 194 SER Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain L residue 6 THR Chi-restraints excluded: chain L residue 12 LEU Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 1.9990 chunk 95 optimal weight: 0.1980 chunk 82 optimal weight: 1.9990 chunk 8 optimal weight: 0.1980 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.0370 chunk 65 optimal weight: 0.3980 chunk 87 optimal weight: 0.0970 chunk 25 optimal weight: 2.9990 overall best weight: 0.1856 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 27 HIS N 3 GLN ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6584 moved from start: 0.5596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8440 Z= 0.169 Angle : 0.656 19.095 11484 Z= 0.310 Chirality : 0.041 0.147 1296 Planarity : 0.004 0.048 1437 Dihedral : 4.731 27.939 1159 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 13.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 2.46 % Allowed : 20.04 % Favored : 77.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.81 (0.26), residues: 1045 helix: 0.63 (0.26), residues: 382 sheet: -0.68 (0.33), residues: 254 loop : -1.48 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.001 TRP H 168 HIS 0.008 0.001 HIS A 27 PHE 0.017 0.001 PHE A 103 TYR 0.026 0.002 TYR A 92 ARG 0.007 0.000 ARG A 264 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2090 Ramachandran restraints generated. 1045 Oldfield, 0 Emsley, 1045 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 190 time to evaluate : 0.788 Fit side-chains revert: symmetry clash REVERT: A -51 LYS cc_start: 0.7791 (tttt) cc_final: 0.7394 (mtmm) REVERT: A -50 MET cc_start: 0.6664 (OUTLIER) cc_final: 0.6303 (tmm) REVERT: A -49 ARG cc_start: 0.7662 (tpt-90) cc_final: 0.7067 (tpp80) REVERT: A 53 LEU cc_start: 0.6345 (mp) cc_final: 0.5724 (mt) REVERT: A 72 LEU cc_start: 0.7282 (tp) cc_final: 0.6991 (tp) REVERT: A 79 VAL cc_start: 0.7895 (m) cc_final: 0.7583 (t) REVERT: A 91 ARG cc_start: 0.7306 (mmt180) cc_final: 0.7065 (mmp80) REVERT: A 99 GLN cc_start: 0.7608 (tt0) cc_final: 0.7041 (tt0) REVERT: A 148 ARG cc_start: 0.6992 (OUTLIER) cc_final: 0.6123 (mtt90) REVERT: A 165 PHE cc_start: 0.7655 (t80) cc_final: 0.7101 (t80) REVERT: A 293 ASN cc_start: 0.7255 (t160) cc_final: 0.6973 (t0) REVERT: A 386 GLN cc_start: 0.7319 (mm-40) cc_final: 0.6997 (tp40) REVERT: A 387 ILE cc_start: 0.7043 (mt) cc_final: 0.6815 (mt) REVERT: H 20 SER cc_start: 0.8217 (m) cc_final: 0.7833 (p) REVERT: H 63 TYR cc_start: 0.7746 (m-10) cc_final: 0.7448 (m-10) REVERT: H 110 TRP cc_start: 0.8317 (t60) cc_final: 0.6913 (t60) REVERT: H 136 PHE cc_start: 0.7344 (m-80) cc_final: 0.7100 (m-80) REVERT: H 206 GLN cc_start: 0.7009 (tt0) cc_final: 0.6773 (tt0) REVERT: N 34 MET cc_start: 0.6254 (mtt) cc_final: 0.6035 (mtt) REVERT: N 83 MET cc_start: 0.6803 (ptm) cc_final: 0.6347 (ppp) REVERT: N 86 LEU cc_start: 0.6991 (tp) cc_final: 0.5186 (tp) REVERT: L 32 SER cc_start: 0.8079 (t) cc_final: 0.7760 (p) REVERT: L 87 TYR cc_start: 0.8596 (m-10) cc_final: 0.8363 (m-80) REVERT: L 94 TYR cc_start: 0.7666 (t80) cc_final: 0.7433 (t80) outliers start: 22 outliers final: 17 residues processed: 202 average time/residue: 0.2043 time to fit residues: 56.5179 Evaluate side-chains 210 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 191 time to evaluate : 0.935 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue -69 LEU Chi-restraints excluded: chain A residue -50 MET Chi-restraints excluded: chain A residue -18 PHE Chi-restraints excluded: chain A residue -11 ILE Chi-restraints excluded: chain A residue -7 LEU Chi-restraints excluded: chain A residue 26 ARG Chi-restraints excluded: chain A residue 27 HIS Chi-restraints excluded: chain A residue 69 THR Chi-restraints excluded: chain A residue 148 ARG Chi-restraints excluded: chain H residue 62 SER Chi-restraints excluded: chain H residue 72 THR Chi-restraints excluded: chain H residue 87 ASN Chi-restraints excluded: chain H residue 121 THR Chi-restraints excluded: chain H residue 160 PHE Chi-restraints excluded: chain H residue 197 THR Chi-restraints excluded: chain H residue 207 THR Chi-restraints excluded: chain L residue 16 VAL Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 53 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 76 optimal weight: 1.9990 chunk 12 optimal weight: 0.0980 chunk 22 optimal weight: 0.3980 chunk 82 optimal weight: 2.9990 chunk 34 optimal weight: 0.0980 chunk 84 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 15 optimal weight: 0.5980 chunk 72 optimal weight: 0.4980 chunk 4 optimal weight: 0.0050 chunk 59 optimal weight: 0.0870 overall best weight: 0.1372 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A -70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.165235 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.146496 restraints weight = 13083.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.150162 restraints weight = 7160.065| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.152601 restraints weight = 4528.187| |-----------------------------------------------------------------------------| r_work (final): 0.3933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6547 moved from start: 0.5534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8440 Z= 0.166 Angle : 0.654 20.750 11484 Z= 0.310 Chirality : 0.041 0.211 1296 Planarity : 0.004 0.048 1437 Dihedral : 4.577 27.654 1159 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer: Outliers : 2.02 % Allowed : 20.60 % Favored : 77.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 6.98 % 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: -0.67 (0.27), residues: 1045 helix: 0.75 (0.26), residues: 383 sheet: -0.55 (0.33), residues: 253 loop : -1.46 (0.32), residues: 409 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.001 TRP H 168 HIS 0.007 0.001 HIS A 27 PHE 0.016 0.001 PHE A 103 TYR 0.022 0.002 TYR A 92 ARG 0.011 0.000 ARG A 264 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2177.67 seconds wall clock time: 40 minutes 15.60 seconds (2415.60 seconds total)