Starting phenix.real_space_refine on Sun Mar 10 21:27:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/03_2024/7yi8_33853_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/03_2024/7yi8_33853.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/03_2024/7yi8_33853.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/03_2024/7yi8_33853.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/03_2024/7yi8_33853_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7yi8_33853/03_2024/7yi8_33853_updated.pdb" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.064 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: 4 Type Number sf(0) Gaussians S 27 5.16 5 C 3334 2.51 5 N 892 2.21 5 O 972 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ASP 384": "OD1" <-> "OD2" Residue "A TYR 405": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 193": "OD1" <-> "OD2" Residue "B ASP 209": "OD1" <-> "OD2" Residue "B TYR 294": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5225 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2117 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2117 Classifications: {'peptide': 257} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 249} Chain breaks: 2 Chain: "B" Number of atoms: 1819 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1819 Classifications: {'peptide': 223} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 215} Chain breaks: 1 Chain: "C" Number of atoms: 269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 32, 269 Classifications: {'peptide': 32} Link IDs: {'TRANS': 31} Chain: "D" Number of atoms: 994 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 994 Classifications: {'peptide': 122} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 120} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Time building chain proxies: 3.87, per 1000 atoms: 0.74 Number of scatterers: 5225 At special positions: 0 Unit cell: (70.55, 73.1, 119.85, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 27 16.00 O 972 8.00 N 892 7.00 C 3334 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 979.8 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1206 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 24 helices and 2 sheets defined 31.2% alpha, 12.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.03 Creating SS restraints... Processing helix chain 'A' and resid 101 through 104 No H-bonds generated for 'chain 'A' and resid 101 through 104' Processing helix chain 'A' and resid 106 through 109 No H-bonds generated for 'chain 'A' and resid 106 through 109' Processing helix chain 'A' and resid 166 through 168 No H-bonds generated for 'chain 'A' and resid 166 through 168' Processing helix chain 'A' and resid 193 through 203 Processing helix chain 'A' and resid 218 through 226 Processing helix chain 'A' and resid 321 through 333 Processing helix chain 'A' and resid 338 through 340 No H-bonds generated for 'chain 'A' and resid 338 through 340' Processing helix chain 'A' and resid 343 through 345 No H-bonds generated for 'chain 'A' and resid 343 through 345' Processing helix chain 'A' and resid 403 through 413 Processing helix chain 'A' and resid 415 through 417 No H-bonds generated for 'chain 'A' and resid 415 through 417' Processing helix chain 'B' and resid 141 through 166 removed outlier: 3.607A pdb=" N ASN B 166 " --> pdb=" O ASN B 162 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 198 Processing helix chain 'B' and resid 232 through 236 Processing helix chain 'B' and resid 240 through 243 No H-bonds generated for 'chain 'B' and resid 240 through 243' Processing helix chain 'B' and resid 255 through 267 removed outlier: 5.361A pdb=" N ARG B 259 " --> pdb=" O ALA B 256 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N VAL B 260 " --> pdb=" O LYS B 257 " (cutoff:3.500A) Processing helix chain 'B' and resid 337 through 345 Processing helix chain 'C' and resid 170 through 182 removed outlier: 4.377A pdb=" N ALA C 175 " --> pdb=" O TYR C 171 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N VAL C 178 " --> pdb=" O LYS C 174 " (cutoff:3.500A) Processing helix chain 'D' and resid 14 through 25 removed outlier: 3.603A pdb=" N LYS D 19 " --> pdb=" O THR D 15 " (cutoff:3.500A) Processing helix chain 'D' and resid 39 through 42 No H-bonds generated for 'chain 'D' and resid 39 through 42' Processing helix chain 'D' and resid 52 through 64 Processing helix chain 'D' and resid 84 through 95 removed outlier: 4.419A pdb=" N CYS D 92 " --> pdb=" O GLU D 88 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N MET D 93 " --> pdb=" O LEU D 89 " (cutoff:3.500A) removed outlier: 3.723A pdb=" N ILE D 94 " --> pdb=" O ARG D 90 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N LEU D 95 " --> pdb=" O THR D 91 " (cutoff:3.500A) Processing helix chain 'D' and resid 101 through 103 No H-bonds generated for 'chain 'D' and resid 101 through 103' Processing helix chain 'D' and resid 113 through 118 Processing helix chain 'D' and resid 126 through 128 No H-bonds generated for 'chain 'D' and resid 126 through 128' Processing sheet with id= A, first strand: chain 'A' and resid 125 through 129 removed outlier: 6.616A pdb=" N ILE A 183 " --> pdb=" O LEU A 147 " (cutoff:3.500A) removed outlier: 7.590A pdb=" N ILE A 149 " --> pdb=" O ILE A 183 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N PHE A 185 " --> pdb=" O ILE A 149 " (cutoff:3.500A) removed outlier: 5.861A pdb=" N ARG A 366 " --> pdb=" O TYR A 207 " (cutoff:3.500A) removed outlier: 5.059A pdb=" N TYR A 207 " --> pdb=" O ARG A 366 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 176 through 180 removed outlier: 6.709A pdb=" N TRP B 365 " --> pdb=" O ILE B 177 " (cutoff:3.500A) removed outlier: 7.167A pdb=" N ILE B 179 " --> pdb=" O TRP B 365 " (cutoff:3.500A) removed outlier: 5.979A pdb=" N SER B 367 " --> pdb=" O ILE B 179 " (cutoff:3.500A) removed outlier: 6.738A pdb=" N TYR B 351 " --> pdb=" O VAL B 366 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE B 368 " --> pdb=" O TYR B 351 " (cutoff:3.500A) removed outlier: 6.640A pdb=" N GLU B 353 " --> pdb=" O ILE B 368 " (cutoff:3.500A) removed outlier: 6.509A pdb=" N VAL B 205 " --> pdb=" O LEU B 352 " (cutoff:3.500A) removed outlier: 8.101A pdb=" N ILE B 354 " --> pdb=" O VAL B 205 " (cutoff:3.500A) removed outlier: 7.046A pdb=" N MET B 207 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.947A pdb=" N PHE B 248 " --> pdb=" O ILE B 206 " (cutoff:3.500A) removed outlier: 8.217A pdb=" N MET B 208 " --> pdb=" O PHE B 248 " (cutoff:3.500A) removed outlier: 6.418A pdb=" N PHE B 250 " --> pdb=" O MET B 208 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N SER B 301 " --> pdb=" O ALA B 253 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N VAL B 306 " --> pdb=" O LEU B 272 " (cutoff:3.500A) removed outlier: 5.512A pdb=" N LEU B 272 " --> pdb=" O VAL B 306 " (cutoff:3.500A) 140 hydrogen bonds defined for protein. 390 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: 1.47 Time building geometry restraints manager: 2.24 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1406 1.33 - 1.45: 870 1.45 - 1.57: 2995 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 5318 Sorted by residual: bond pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " ideal model delta sigma weight residual 1.322 1.381 -0.059 2.00e-02 2.50e+03 8.61e+00 bond pdb=" C8 SAH B 401 " pdb=" N7 SAH B 401 " ideal model delta sigma weight residual 1.299 1.351 -0.052 2.00e-02 2.50e+03 6.66e+00 bond pdb=" C2 SAH B 401 " pdb=" N1 SAH B 401 " ideal model delta sigma weight residual 1.330 1.379 -0.049 2.00e-02 2.50e+03 5.89e+00 bond pdb=" C6 SAH B 401 " pdb=" N1 SAH B 401 " ideal model delta sigma weight residual 1.338 1.378 -0.040 2.00e-02 2.50e+03 4.10e+00 bond pdb=" C1' SAH B 401 " pdb=" N9 SAH B 401 " ideal model delta sigma weight residual 1.440 1.476 -0.036 2.00e-02 2.50e+03 3.24e+00 ... (remaining 5313 not shown) Histogram of bond angle deviations from ideal: 91.43 - 99.94: 3 99.94 - 108.46: 211 108.46 - 116.97: 3554 116.97 - 125.49: 3303 125.49 - 134.00: 76 Bond angle restraints: 7147 Sorted by residual: angle pdb=" CG SAH B 401 " pdb=" SD SAH B 401 " pdb=" C5' SAH B 401 " ideal model delta sigma weight residual 101.77 91.43 10.34 3.00e+00 1.11e-01 1.19e+01 angle pdb=" O SAH B 401 " pdb=" C SAH B 401 " pdb=" OXT SAH B 401 " ideal model delta sigma weight residual 126.79 117.95 8.84 3.00e+00 1.11e-01 8.67e+00 angle pdb=" C LYS B 317 " pdb=" N ASN B 318 " pdb=" CA ASN B 318 " ideal model delta sigma weight residual 121.54 126.99 -5.45 1.91e+00 2.74e-01 8.14e+00 angle pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " pdb=" C4 SAH B 401 " ideal model delta sigma weight residual 111.67 120.13 -8.46 3.00e+00 1.11e-01 7.96e+00 angle pdb=" N1 SAH B 401 " pdb=" C2 SAH B 401 " pdb=" N3 SAH B 401 " ideal model delta sigma weight residual 128.45 120.52 7.93 3.00e+00 1.11e-01 6.99e+00 ... (remaining 7142 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.61: 2895 17.61 - 35.23: 266 35.23 - 52.84: 60 52.84 - 70.45: 10 70.45 - 88.07: 6 Dihedral angle restraints: 3237 sinusoidal: 1382 harmonic: 1855 Sorted by residual: dihedral pdb=" CA MET A 401 " pdb=" C MET A 401 " pdb=" N MET A 402 " pdb=" CA MET A 402 " ideal model delta harmonic sigma weight residual 180.00 163.78 16.22 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CG ARG B 357 " pdb=" CD ARG B 357 " pdb=" NE ARG B 357 " pdb=" CZ ARG B 357 " ideal model delta sinusoidal sigma weight residual -90.00 -134.61 44.61 2 1.50e+01 4.44e-03 1.05e+01 dihedral pdb=" CB GLU A 201 " pdb=" CG GLU A 201 " pdb=" CD GLU A 201 " pdb=" OE1 GLU A 201 " ideal model delta sinusoidal sigma weight residual 0.00 -88.07 88.07 1 3.00e+01 1.11e-03 1.03e+01 ... (remaining 3234 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 489 0.034 - 0.068: 212 0.068 - 0.102: 50 0.102 - 0.136: 26 0.136 - 0.170: 3 Chirality restraints: 780 Sorted by residual: chirality pdb=" CB VAL B 310 " pdb=" CA VAL B 310 " pdb=" CG1 VAL B 310 " pdb=" CG2 VAL B 310 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.22e-01 chirality pdb=" CA GLN B 155 " pdb=" N GLN B 155 " pdb=" C GLN B 155 " pdb=" CB GLN B 155 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.11e-01 chirality pdb=" CA ILE A 112 " pdb=" N ILE A 112 " pdb=" C ILE A 112 " pdb=" CB ILE A 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 ... (remaining 777 not shown) Planarity restraints: 909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 151 " -0.011 2.00e-02 2.50e+03 2.28e-02 5.22e+00 pdb=" C LEU B 151 " 0.040 2.00e-02 2.50e+03 pdb=" O LEU B 151 " -0.015 2.00e-02 2.50e+03 pdb=" N HIS B 152 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR A 352 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.51e+00 pdb=" N PRO A 353 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 353 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 353 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR D 51 " 0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO D 52 " -0.072 5.00e-02 4.00e+02 pdb=" CA PRO D 52 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 52 " 0.023 5.00e-02 4.00e+02 ... (remaining 906 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 203 2.72 - 3.27: 5188 3.27 - 3.81: 8170 3.81 - 4.36: 10546 4.36 - 4.90: 17653 Nonbonded interactions: 41760 Sorted by model distance: nonbonded pdb=" OG SER B 326 " pdb=" OE2 GLU B 337 " model vdw 2.179 2.440 nonbonded pdb=" O LYS B 257 " pdb=" OG1 THR B 261 " model vdw 2.204 2.440 nonbonded pdb=" OG SER A 383 " pdb=" NZ LYS B 289 " model vdw 2.257 2.520 nonbonded pdb=" O CYS B 346 " pdb=" OH TYR B 351 " model vdw 2.258 2.440 nonbonded pdb=" OH TYR A 407 " pdb=" OE1 GLU A 431 " model vdw 2.286 2.440 ... (remaining 41755 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 individual isotropic 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: 1.090 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: 0.000 Extract box with map and model: 3.250 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.570 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.020 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:18.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7157 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 : 0.003 0.059 5318 Z= 0.187 Angle : 0.608 10.344 7147 Z= 0.301 Chirality : 0.043 0.170 780 Planarity : 0.004 0.047 909 Dihedral : 14.732 88.067 2031 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.33), residues: 620 helix: 0.07 (0.37), residues: 193 sheet: -0.33 (0.47), residues: 104 loop : -0.51 (0.36), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 107 HIS 0.003 0.001 HIS B 152 PHE 0.012 0.001 PHE A 355 TYR 0.013 0.001 TYR A 352 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.645 Fit side-chains REVERT: A 384 ASP cc_start: 0.7231 (t70) cc_final: 0.6985 (t0) REVERT: A 405 TYR cc_start: 0.7434 (t80) cc_final: 0.7153 (t80) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 1.1288 time to fit residues: 144.9112 Evaluate side-chains 80 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 48 optimal weight: 1.9990 chunk 18 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 36 optimal weight: 3.9990 chunk 56 optimal weight: 5.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 323 GLN ** B 155 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 343 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 83 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5318 Z= 0.314 Angle : 0.636 8.349 7147 Z= 0.328 Chirality : 0.044 0.157 780 Planarity : 0.004 0.059 909 Dihedral : 5.163 44.064 676 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 3.99 % Allowed : 14.04 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.33), residues: 620 helix: -0.34 (0.36), residues: 192 sheet: -0.33 (0.48), residues: 104 loop : -0.57 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP B 252 HIS 0.003 0.001 HIS A 360 PHE 0.015 0.002 PHE B 293 TYR 0.017 0.002 TYR A 352 ARG 0.006 0.001 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 84 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: B 353 GLU cc_start: 0.7553 (OUTLIER) cc_final: 0.7271 (tt0) REVERT: D 108 ILE cc_start: 0.7111 (mp) cc_final: 0.6725 (mt) outliers start: 23 outliers final: 12 residues processed: 98 average time/residue: 1.1102 time to fit residues: 113.9608 Evaluate side-chains 89 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 76 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 31 optimal weight: 2.9990 chunk 17 optimal weight: 0.8980 chunk 46 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 chunk 15 optimal weight: 4.9990 chunk 56 optimal weight: 0.9990 chunk 60 optimal weight: 6.9990 chunk 50 optimal weight: 3.9990 chunk 55 optimal weight: 4.9990 chunk 19 optimal weight: 3.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 226 ASN A 380 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 20 ASN ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 113 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.1772 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5318 Z= 0.230 Angle : 0.564 7.183 7147 Z= 0.293 Chirality : 0.042 0.146 780 Planarity : 0.004 0.055 909 Dihedral : 5.046 47.974 676 Min Nonbonded Distance : 2.172 Molprobity Statistics. All-atom Clashscore : 12.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 4.33 % Allowed : 16.46 % Favored : 79.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.33), residues: 620 helix: -0.32 (0.36), residues: 190 sheet: -0.31 (0.49), residues: 105 loop : -0.58 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 252 HIS 0.003 0.001 HIS A 360 PHE 0.011 0.002 PHE A 355 TYR 0.016 0.002 TYR A 207 ARG 0.004 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 80 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: A 429 MET cc_start: 0.7369 (mtt) cc_final: 0.7140 (mtt) REVERT: B 353 GLU cc_start: 0.7572 (OUTLIER) cc_final: 0.7292 (tt0) outliers start: 25 outliers final: 16 residues processed: 96 average time/residue: 1.1926 time to fit residues: 120.1108 Evaluate side-chains 88 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain B residue 363 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 55 optimal weight: 10.0000 chunk 42 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 6 optimal weight: 0.0980 chunk 26 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 6.9990 chunk 53 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7334 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5318 Z= 0.227 Angle : 0.557 6.766 7147 Z= 0.288 Chirality : 0.041 0.141 780 Planarity : 0.004 0.054 909 Dihedral : 4.984 46.724 676 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 5.55 % Allowed : 16.81 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.33), residues: 620 helix: -0.45 (0.36), residues: 197 sheet: -0.13 (0.51), residues: 98 loop : -0.69 (0.35), residues: 325 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 365 HIS 0.002 0.001 HIS A 360 PHE 0.030 0.002 PHE B 203 TYR 0.017 0.002 TYR A 207 ARG 0.004 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 73 time to evaluate : 0.667 Fit side-chains revert: symmetry clash REVERT: B 353 GLU cc_start: 0.7494 (OUTLIER) cc_final: 0.7216 (tt0) outliers start: 32 outliers final: 20 residues processed: 97 average time/residue: 0.9915 time to fit residues: 101.3841 Evaluate side-chains 96 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 275 GLU Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 34 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 51 optimal weight: 4.9990 chunk 41 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 53 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7369 moved from start: 0.2127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5318 Z= 0.273 Angle : 0.598 7.196 7147 Z= 0.308 Chirality : 0.043 0.151 780 Planarity : 0.004 0.057 909 Dihedral : 5.065 40.474 676 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 5.55 % Allowed : 18.54 % Favored : 75.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.33), residues: 620 helix: -0.55 (0.35), residues: 199 sheet: -0.41 (0.52), residues: 95 loop : -0.72 (0.35), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 365 HIS 0.004 0.001 HIS C 169 PHE 0.027 0.002 PHE B 203 TYR 0.019 0.002 TYR A 352 ARG 0.004 0.001 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 75 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: B 353 GLU cc_start: 0.7578 (OUTLIER) cc_final: 0.7288 (tt0) outliers start: 32 outliers final: 21 residues processed: 97 average time/residue: 1.0201 time to fit residues: 104.5017 Evaluate side-chains 95 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 0.658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 264 MET Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 309 ASP Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 353 GLU Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 35 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 5.9990 chunk 49 optimal weight: 8.9990 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 6 optimal weight: 0.0170 chunk 34 optimal weight: 0.5980 overall best weight: 0.6218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 171 ASN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7293 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5318 Z= 0.153 Angle : 0.510 7.002 7147 Z= 0.265 Chirality : 0.040 0.165 780 Planarity : 0.004 0.054 909 Dihedral : 4.786 47.493 676 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 4.16 % Allowed : 20.62 % Favored : 75.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.83 (0.33), residues: 620 helix: -0.31 (0.37), residues: 198 sheet: -0.34 (0.53), residues: 95 loop : -0.68 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 365 HIS 0.002 0.000 HIS A 360 PHE 0.030 0.002 PHE B 203 TYR 0.019 0.001 TYR A 207 ARG 0.003 0.000 ARG A 108 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 0.677 Fit side-chains revert: symmetry clash REVERT: A 173 LYS cc_start: 0.7219 (OUTLIER) cc_final: 0.6986 (mmtm) REVERT: A 191 GLU cc_start: 0.7725 (OUTLIER) cc_final: 0.6870 (mp0) outliers start: 24 outliers final: 14 residues processed: 95 average time/residue: 0.9785 time to fit residues: 98.0675 Evaluate side-chains 89 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 73 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 173 LYS Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 43 optimal weight: 2.9990 chunk 33 optimal weight: 0.0970 chunk 50 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 1.9990 chunk 27 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 35 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7372 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 5318 Z= 0.284 Angle : 0.606 7.477 7147 Z= 0.311 Chirality : 0.043 0.160 780 Planarity : 0.004 0.057 909 Dihedral : 4.981 35.883 676 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 4.68 % Allowed : 20.80 % Favored : 74.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.01 (0.33), residues: 620 helix: -0.53 (0.36), residues: 198 sheet: -0.30 (0.53), residues: 95 loop : -0.78 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 365 HIS 0.003 0.001 HIS A 360 PHE 0.045 0.002 PHE B 203 TYR 0.022 0.002 TYR A 352 ARG 0.004 0.000 ARG D 22 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 72 time to evaluate : 0.684 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7744 (OUTLIER) cc_final: 0.6928 (mp0) outliers start: 27 outliers final: 19 residues processed: 90 average time/residue: 0.9825 time to fit residues: 93.1491 Evaluate side-chains 92 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 24 ASP Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 11 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 40 optimal weight: 0.7980 chunk 29 optimal weight: 0.6980 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 1.9990 chunk 52 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7355 moved from start: 0.2294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5318 Z= 0.242 Angle : 0.588 8.097 7147 Z= 0.302 Chirality : 0.042 0.170 780 Planarity : 0.004 0.058 909 Dihedral : 4.942 38.493 676 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 12.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.33 % Allowed : 22.01 % Favored : 73.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.33), residues: 620 helix: -0.52 (0.36), residues: 198 sheet: -0.30 (0.53), residues: 95 loop : -0.79 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP B 365 HIS 0.002 0.001 HIS A 360 PHE 0.039 0.002 PHE B 203 TYR 0.021 0.002 TYR A 352 ARG 0.004 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 71 time to evaluate : 0.643 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7736 (OUTLIER) cc_final: 0.6877 (mp0) outliers start: 25 outliers final: 19 residues processed: 91 average time/residue: 0.9016 time to fit residues: 86.8853 Evaluate side-chains 89 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 348 LEU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 437 ASP Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 chunk 55 optimal weight: 0.0670 chunk 36 optimal weight: 0.4980 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 40 optimal weight: 2.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7279 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5318 Z= 0.147 Angle : 0.514 8.255 7147 Z= 0.262 Chirality : 0.040 0.176 780 Planarity : 0.004 0.055 909 Dihedral : 4.696 46.115 676 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 11.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 4.16 % Allowed : 22.01 % Favored : 73.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.33), residues: 620 helix: -0.25 (0.37), residues: 198 sheet: -0.20 (0.53), residues: 95 loop : -0.74 (0.34), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 365 HIS 0.001 0.000 HIS A 360 PHE 0.029 0.001 PHE B 203 TYR 0.020 0.001 TYR A 207 ARG 0.004 0.000 ARG B 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 0.683 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7717 (OUTLIER) cc_final: 0.6781 (mp0) REVERT: D 108 ILE cc_start: 0.7289 (mp) cc_final: 0.7050 (mt) outliers start: 24 outliers final: 15 residues processed: 91 average time/residue: 0.9171 time to fit residues: 88.3227 Evaluate side-chains 88 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.588 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 61 optimal weight: 2.9990 chunk 56 optimal weight: 0.6980 chunk 49 optimal weight: 6.9990 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 7 optimal weight: 0.5980 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7398 moved from start: 0.2502 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5318 Z= 0.351 Angle : 0.672 8.224 7147 Z= 0.338 Chirality : 0.045 0.221 780 Planarity : 0.005 0.061 909 Dihedral : 5.146 37.092 676 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 13.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.64 % Allowed : 22.88 % Favored : 73.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.10 (0.33), residues: 620 helix: -0.63 (0.35), residues: 197 sheet: -0.32 (0.53), residues: 95 loop : -0.84 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 365 HIS 0.003 0.001 HIS A 360 PHE 0.042 0.003 PHE B 203 TYR 0.027 0.002 TYR A 352 ARG 0.006 0.001 ARG D 22 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 72 time to evaluate : 0.656 Fit side-chains revert: symmetry clash REVERT: A 191 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.6961 (mp0) REVERT: D 108 ILE cc_start: 0.7408 (mp) cc_final: 0.7182 (mt) outliers start: 21 outliers final: 19 residues processed: 88 average time/residue: 0.9350 time to fit residues: 87.1356 Evaluate side-chains 92 residues out of total 578 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 139 LYS Chi-restraints excluded: chain A residue 168 ASP Chi-restraints excluded: chain A residue 181 ASN Chi-restraints excluded: chain A residue 191 GLU Chi-restraints excluded: chain A residue 341 THR Chi-restraints excluded: chain A residue 389 VAL Chi-restraints excluded: chain A residue 398 VAL Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain B residue 151 LEU Chi-restraints excluded: chain B residue 155 GLN Chi-restraints excluded: chain B residue 260 VAL Chi-restraints excluded: chain B residue 277 THR Chi-restraints excluded: chain B residue 284 ASN Chi-restraints excluded: chain B residue 310 VAL Chi-restraints excluded: chain B residue 321 SER Chi-restraints excluded: chain B residue 359 ASN Chi-restraints excluded: chain C residue 166 ILE Chi-restraints excluded: chain D residue 44 THR Chi-restraints excluded: chain D residue 51 THR Chi-restraints excluded: chain D residue 62 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 62 random chunks: chunk 13 optimal weight: 0.8980 chunk 49 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 50 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 chunk 43 optimal weight: 0.9980 chunk 2 optimal weight: 9.9990 chunk 35 optimal weight: 2.9990 chunk 56 optimal weight: 0.5980 chunk 33 optimal weight: 0.0670 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 171 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 98 ASN ** 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 = 0.4295 r_free = 0.4295 target = 0.185500 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.151038 restraints weight = 6080.287| |-----------------------------------------------------------------------------| r_work (start): 0.3931 rms_B_bonded: 2.40 r_work: 0.3716 rms_B_bonded: 2.80 restraints_weight: 0.5000 r_work: 0.3573 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3573 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.2318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5318 Z= 0.165 Angle : 0.550 8.586 7147 Z= 0.275 Chirality : 0.041 0.187 780 Planarity : 0.004 0.055 909 Dihedral : 4.845 48.023 676 Min Nonbonded Distance : 2.186 Molprobity Statistics. All-atom Clashscore : 11.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.71 % Favored : 96.29 % Rotamer: Outliers : 3.47 % Allowed : 23.57 % Favored : 72.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.33), residues: 620 helix: -0.31 (0.37), residues: 197 sheet: -0.20 (0.54), residues: 95 loop : -0.77 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 365 HIS 0.002 0.000 HIS D 39 PHE 0.029 0.002 PHE B 203 TYR 0.021 0.001 TYR A 207 ARG 0.004 0.000 ARG B 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2465.06 seconds wall clock time: 44 minutes 24.93 seconds (2664.93 seconds total)