Starting phenix.real_space_refine on Tue Nov 14 08:56:55 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2023/8hik_34819_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2023/8hik_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_34819/11_2023/8hik_34819.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2023/8hik_34819.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2023/8hik_34819_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hik_34819/11_2023/8hik_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-1.21rc1-5144/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: 4.93, per 1000 atoms: 0.60 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: 3.22 Conformation dependent library (CDL) restraints added in 1.6 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: 1.80 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: 2.26 Time building geometry restraints manager: 3.47 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: 1.820 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.870 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 26.360 Find NCS groups from input model: 0.230 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:2.790 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.310 ------------------------------------------------------------------------------- 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 *********************** 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 : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 217 average time/residue: 0.1996 time to fit residues: 59.2558 Evaluate side-chains 178 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 178 time to evaluate : 0.814 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1587 ------------------------------------------------------------------------------- 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: 0.4980 chunk 43 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 53 optimal weight: 0.9990 chunk 42 optimal weight: 0.4980 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 60 optimal weight: 0.4980 chunk 94 optimal weight: 0.5980 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 -77 ASN A 66 ASN A 120 GLN A 289 HIS A 358 HIS A 431 GLN H 178 HIS ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 28 GLN L 90 GLN L 162 GLN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 191 HIS Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6441 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 8440 Z= 0.251 Angle : 0.599 7.987 11484 Z= 0.307 Chirality : 0.041 0.150 1296 Planarity : 0.005 0.050 1437 Dihedral : 5.130 46.460 1159 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 2.35 % Allowed : 10.53 % Favored : 87.12 % 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: -2.10 (0.25), residues: 1045 helix: -0.21 (0.26), residues: 374 sheet: -1.51 (0.31), residues: 244 loop : -2.33 (0.28), residues: 427 *********************** 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 237 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 216 time to evaluate : 0.926 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 224 average time/residue: 0.1963 time to fit residues: 61.0838 Evaluate side-chains 205 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 195 time to evaluate : 0.870 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1248 time to fit residues: 3.1890 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 52 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 78 optimal weight: 0.0070 chunk 64 optimal weight: 0.0980 chunk 26 optimal weight: 0.6980 chunk 94 optimal weight: 1.9990 chunk 102 optimal weight: 0.8980 chunk 84 optimal weight: 1.9990 chunk 93 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 75 optimal weight: 0.0770 overall best weight: 0.2156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -20 HIS A 66 ASN A 377 GLN H 214 HIS L 28 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6406 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.041 8440 Z= 0.156 Angle : 0.573 12.146 11484 Z= 0.280 Chirality : 0.040 0.145 1296 Planarity : 0.004 0.046 1437 Dihedral : 4.747 43.848 1159 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 1.57 % Allowed : 13.10 % Favored : 85.33 % 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: -1.44 (0.26), residues: 1045 helix: 0.40 (0.26), residues: 378 sheet: -1.07 (0.32), residues: 244 loop : -2.11 (0.29), residues: 423 *********************** 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 220 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 206 time to evaluate : 0.788 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 7 residues processed: 210 average time/residue: 0.2004 time to fit residues: 57.7298 Evaluate side-chains 194 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 187 time to evaluate : 0.847 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0826 time to fit residues: 2.2847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 93 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 49 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 63 optimal weight: 0.1980 chunk 94 optimal weight: 0.7980 chunk 100 optimal weight: 0.5980 chunk 89 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 83 optimal weight: 1.9990 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 -77 ASN H 169 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 moved from start: 0.4170 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.079 8440 Z= 0.295 Angle : 0.652 8.143 11484 Z= 0.330 Chirality : 0.043 0.156 1296 Planarity : 0.004 0.083 1437 Dihedral : 5.059 33.049 1159 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 13.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 2.80 % Allowed : 13.33 % Favored : 83.87 % 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: -1.36 (0.26), residues: 1045 helix: 0.36 (0.26), residues: 381 sheet: -0.99 (0.33), residues: 246 loop : -1.99 (0.31), residues: 418 *********************** 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 229 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 204 time to evaluate : 0.932 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 25 outliers final: 10 residues processed: 212 average time/residue: 0.1792 time to fit residues: 53.6855 Evaluate side-chains 199 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 189 time to evaluate : 0.876 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1241 time to fit residues: 3.1446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 41 optimal weight: 0.6980 chunk 85 optimal weight: 0.6980 chunk 69 optimal weight: 0.9990 chunk 0 optimal weight: 0.6980 chunk 51 optimal weight: 0.6980 chunk 90 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 GLN A 40 GLN A 377 GLN L 160 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6613 moved from start: 0.4818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 8440 Z= 0.302 Angle : 0.659 9.258 11484 Z= 0.334 Chirality : 0.043 0.141 1296 Planarity : 0.004 0.077 1437 Dihedral : 5.050 25.633 1159 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 15.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.03 % Favored : 93.97 % Rotamer: Outliers : 2.35 % Allowed : 16.24 % Favored : 81.41 % 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: -1.53 (0.25), residues: 1045 helix: 0.11 (0.25), residues: 385 sheet: -1.01 (0.32), residues: 245 loop : -2.04 (0.30), residues: 415 *********************** 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 229 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 208 time to evaluate : 0.900 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 9 residues processed: 216 average time/residue: 0.2050 time to fit residues: 61.4900 Evaluate side-chains 210 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 201 time to evaluate : 0.905 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0888 time to fit residues: 2.7749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.0060 chunk 59 optimal weight: 0.0470 chunk 24 optimal weight: 1.9990 chunk 100 optimal weight: 0.9990 chunk 83 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 0.2980 chunk 52 optimal weight: 0.5980 chunk 97 optimal weight: 0.4980 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 160 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6553 moved from start: 0.4855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8440 Z= 0.192 Angle : 0.607 9.893 11484 Z= 0.301 Chirality : 0.040 0.169 1296 Planarity : 0.004 0.070 1437 Dihedral : 4.799 22.723 1159 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 13.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 1.68 % Allowed : 17.58 % Favored : 80.74 % 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: 0.27 (0.25), residues: 382 sheet: -0.83 (0.33), residues: 244 loop : -1.80 (0.31), residues: 419 *********************** 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 218 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 203 time to evaluate : 0.893 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 10 residues processed: 206 average time/residue: 0.2164 time to fit residues: 60.7682 Evaluate side-chains 207 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0799 time to fit residues: 2.7488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 11 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 84 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 62 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 46 optimal weight: 0.6980 chunk 40 optimal weight: 0.2980 chunk 59 optimal weight: 0.2980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS L 160 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6587 moved from start: 0.5174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 8440 Z= 0.235 Angle : 0.638 9.572 11484 Z= 0.316 Chirality : 0.041 0.161 1296 Planarity : 0.004 0.070 1437 Dihedral : 4.838 21.826 1159 Min Nonbonded Distance : 2.128 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 1.12 % Allowed : 19.48 % Favored : 79.40 % 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: -1.20 (0.26), residues: 1045 helix: 0.29 (0.26), residues: 381 sheet: -0.80 (0.33), residues: 245 loop : -1.75 (0.31), residues: 419 *********************** 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 207 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 197 time to evaluate : 0.847 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 200 average time/residue: 0.2083 time to fit residues: 57.1401 Evaluate side-chains 194 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 188 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0880 time to fit residues: 2.2130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 63 optimal weight: 2.9990 chunk 68 optimal weight: 0.0270 chunk 49 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 78 optimal weight: 0.0870 chunk 91 optimal weight: 0.5980 chunk 96 optimal weight: 0.4980 chunk 87 optimal weight: 0.8980 chunk 93 optimal weight: 0.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 277 ASN L 4 GLN L 160 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6563 moved from start: 0.5284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.061 8440 Z= 0.208 Angle : 0.659 14.963 11484 Z= 0.319 Chirality : 0.042 0.197 1296 Planarity : 0.004 0.069 1437 Dihedral : 4.763 21.606 1159 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 14.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.01 % Allowed : 20.16 % Favored : 78.84 % 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: -1.01 (0.26), residues: 1045 helix: 0.49 (0.26), residues: 381 sheet: -0.69 (0.33), residues: 254 loop : -1.70 (0.31), residues: 410 *********************** 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 200 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 191 time to evaluate : 0.889 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 194 average time/residue: 0.2076 time to fit residues: 54.9595 Evaluate side-chains 197 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 193 time to evaluate : 0.889 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0905 time to fit residues: 1.8757 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 96 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 73 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 84 optimal weight: 0.3980 chunk 88 optimal weight: 0.4980 chunk 93 optimal weight: 1.9990 chunk 61 optimal weight: 1.9990 chunk 98 optimal weight: 0.3980 chunk 60 optimal weight: 0.6980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 27 HIS ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 160 ASN ** L 168 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: 0.6613 moved from start: 0.5549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 8440 Z= 0.265 Angle : 0.689 14.767 11484 Z= 0.337 Chirality : 0.043 0.199 1296 Planarity : 0.004 0.069 1437 Dihedral : 4.935 23.450 1159 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 16.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 1.34 % Allowed : 20.38 % Favored : 78.28 % 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: -1.06 (0.26), residues: 1045 helix: 0.35 (0.26), residues: 386 sheet: -0.71 (0.33), residues: 249 loop : -1.64 (0.32), residues: 410 *********************** 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 212 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 200 time to evaluate : 0.739 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 12 outliers final: 9 residues processed: 204 average time/residue: 0.2023 time to fit residues: 56.8351 Evaluate side-chains 206 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 197 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0787 time to fit residues: 2.5349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 104 random chunks: chunk 46 optimal weight: 0.8980 chunk 68 optimal weight: 0.8980 chunk 103 optimal weight: 0.7980 chunk 95 optimal weight: 0.3980 chunk 82 optimal weight: 0.0980 chunk 8 optimal weight: 0.0270 chunk 63 optimal weight: 0.8980 chunk 50 optimal weight: 0.0000 chunk 65 optimal weight: 0.1980 chunk 87 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 overall best weight: 0.1442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 40 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 386 GLN ** A 431 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 160 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6509 moved from start: 0.5430 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8440 Z= 0.167 Angle : 0.669 13.505 11484 Z= 0.319 Chirality : 0.041 0.167 1296 Planarity : 0.004 0.068 1437 Dihedral : 4.629 24.867 1159 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 13.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 0.67 % Allowed : 22.06 % Favored : 77.27 % 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: -0.84 (0.26), residues: 1045 helix: 0.68 (0.26), residues: 377 sheet: -0.70 (0.33), residues: 244 loop : -1.55 (0.31), residues: 424 ********************** 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 196 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 190 time to evaluate : 0.917 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 191 average time/residue: 0.2039 time to fit residues: 53.6346 Evaluate side-chains 186 residues out of total 893 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 182 time to evaluate : 0.793 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1097 time to fit residues: 1.8482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9990 chunk 22 optimal weight: 0.7980 chunk 82 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 84 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 15 optimal weight: 0.7980 chunk 72 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 59 optimal weight: 0.0070 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A -77 ASN A 27 HIS ** H 214 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 39 GLN L 160 ASN ** L 168 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 201 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4055 r_free = 0.4055 target = 0.161209 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3812 r_free = 0.3812 target = 0.142581 restraints weight = 12950.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.146330 restraints weight = 7089.807| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.148779 restraints weight = 4449.893| |-----------------------------------------------------------------------------| r_work (final): 0.3875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6623 moved from start: 0.5850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.083 8440 Z= 0.313 Angle : 0.732 13.498 11484 Z= 0.360 Chirality : 0.044 0.212 1296 Planarity : 0.005 0.067 1437 Dihedral : 5.163 27.136 1159 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 18.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.78 % Allowed : 22.51 % Favored : 76.71 % 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: -1.01 (0.26), residues: 1045 helix: 0.37 (0.26), residues: 378 sheet: -0.77 (0.33), residues: 244 loop : -1.49 (0.32), residues: 423 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2236.64 seconds wall clock time: 41 minutes 14.10 seconds (2474.10 seconds total)