Starting phenix.real_space_refine on Wed Mar 5 17:01:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8thr_41269/03_2025/8thr_41269.cif Found real_map, /net/cci-nas-00/data/ceres_data/8thr_41269/03_2025/8thr_41269.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.12 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8thr_41269/03_2025/8thr_41269.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8thr_41269/03_2025/8thr_41269.map" model { file = "/net/cci-nas-00/data/ceres_data/8thr_41269/03_2025/8thr_41269.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8thr_41269/03_2025/8thr_41269.cif" } resolution = 3.12 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= 0.027 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 28 5.16 5 C 1954 2.51 5 N 454 2.21 5 O 501 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2937 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2914 Number of conformers: 1 Conformer: "" Number of residues, atoms: 389, 2914 Classifications: {'peptide': 389} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 23, 'TRANS': 365} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "A" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 23 Unusual residues: {'EBZ': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.42, per 1000 atoms: 1.16 Number of scatterers: 2937 At special positions: 0 Unit cell: (56.936, 71.817, 75.699, 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 28 16.00 O 501 8.00 N 454 7.00 C 1954 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.83 Conformation dependent library (CDL) restraints added in 386.5 milliseconds 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 702 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 0 sheets defined 89.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 17 through 40 removed outlier: 4.139A pdb=" N LEU A 23 " --> pdb=" O ARG A 19 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N PHE A 24 " --> pdb=" O LYS A 20 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N ASP A 33 " --> pdb=" O ALA A 29 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N THR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) removed outlier: 3.997A pdb=" N VAL A 40 " --> pdb=" O LEU A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 47 Proline residue: A 45 - end of helix Processing helix chain 'A' and resid 123 through 128 Processing helix chain 'A' and resid 128 through 157 removed outlier: 3.586A pdb=" N LEU A 134 " --> pdb=" O GLN A 130 " (cutoff:3.500A) removed outlier: 4.039A pdb=" N LYS A 138 " --> pdb=" O LEU A 134 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N ALA A 139 " --> pdb=" O PHE A 135 " (cutoff:3.500A) Proline residue: A 147 - end of helix removed outlier: 3.942A pdb=" N ASN A 154 " --> pdb=" O GLY A 150 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ARG A 155 " --> pdb=" O LEU A 151 " (cutoff:3.500A) Processing helix chain 'A' and resid 158 through 177 removed outlier: 3.811A pdb=" N MET A 169 " --> pdb=" O GLY A 165 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N ALA A 177 " --> pdb=" O THR A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 3.574A pdb=" N LEU A 185 " --> pdb=" O SER A 181 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ALA A 202 " --> pdb=" O CYS A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 213 through 246 removed outlier: 3.750A pdb=" N GLY A 227 " --> pdb=" O ILE A 223 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N LEU A 228 " --> pdb=" O ALA A 224 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N LEU A 233 " --> pdb=" O ALA A 229 " (cutoff:3.500A) Proline residue: A 236 - end of helix Processing helix chain 'A' and resid 249 through 270 removed outlier: 3.929A pdb=" N LEU A 253 " --> pdb=" O THR A 249 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N LEU A 255 " --> pdb=" O PRO A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 284 through 290 removed outlier: 3.743A pdb=" N LEU A 288 " --> pdb=" O PRO A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 312 removed outlier: 3.753A pdb=" N LEU A 295 " --> pdb=" O ASP A 291 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ASN A 305 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N GLY A 307 " --> pdb=" O PHE A 303 " (cutoff:3.500A) removed outlier: 4.228A pdb=" N ILE A 308 " --> pdb=" O ALA A 304 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N LEU A 311 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 313 through 315 No H-bonds generated for 'chain 'A' and resid 313 through 315' Processing helix chain 'A' and resid 319 through 323 removed outlier: 3.900A pdb=" N THR A 322 " --> pdb=" O MET A 319 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 330 Processing helix chain 'A' and resid 331 through 333 No H-bonds generated for 'chain 'A' and resid 331 through 333' Processing helix chain 'A' and resid 334 through 356 removed outlier: 3.911A pdb=" N LEU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ILE A 350 " --> pdb=" O ASN A 346 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N ALA A 352 " --> pdb=" O PHE A 348 " (cutoff:3.500A) removed outlier: 4.782A pdb=" N HIS A 353 " --> pdb=" O GLY A 349 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LYS A 354 " --> pdb=" O ILE A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 373 removed outlier: 3.577A pdb=" N GLY A 364 " --> pdb=" O CYS A 360 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ILE A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.894A pdb=" N VAL A 368 " --> pdb=" O GLY A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 378 Processing helix chain 'A' and resid 380 through 383 Processing helix chain 'A' and resid 384 through 414 Proline residue: A 404 - end of helix removed outlier: 3.834A pdb=" N GLY A 407 " --> pdb=" O MET A 403 " (cutoff:3.500A) Processing helix chain 'A' and resid 420 through 436 removed outlier: 4.293A pdb=" N GLY A 432 " --> pdb=" O ALA A 428 " (cutoff:3.500A) removed outlier: 4.995A pdb=" N TYR A 433 " --> pdb=" O PHE A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 440 through 445 removed outlier: 4.144A pdb=" N ALA A 444 " --> pdb=" O GLY A 440 " (cutoff:3.500A) removed outlier: 3.703A pdb=" N LYS A 445 " --> pdb=" O GLY A 441 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 440 through 445' Processing helix chain 'A' and resid 448 through 462 removed outlier: 3.944A pdb=" N LEU A 452 " --> pdb=" O GLY A 448 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N ASP A 460 " --> pdb=" O ILE A 456 " (cutoff:3.500A) Processing helix chain 'A' and resid 463 through 471 removed outlier: 3.642A pdb=" N CYS A 467 " --> pdb=" O ALA A 464 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 469 " --> pdb=" O LEU A 466 " (cutoff:3.500A) 207 hydrogen bonds defined for protein. 582 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: 0.80 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 498 1.32 - 1.45: 745 1.45 - 1.57: 1716 1.57 - 1.70: 0 1.70 - 1.82: 48 Bond restraints: 3007 Sorted by residual: bond pdb=" CA VAL A 220 " pdb=" CB VAL A 220 " ideal model delta sigma weight residual 1.539 1.491 0.049 1.20e-02 6.94e+03 1.65e+01 bond pdb=" N PRO A 437 " pdb=" CD PRO A 437 " ideal model delta sigma weight residual 1.473 1.427 0.046 1.40e-02 5.10e+03 1.09e+01 bond pdb=" N PRO A 313 " pdb=" CD PRO A 313 " ideal model delta sigma weight residual 1.473 1.428 0.045 1.40e-02 5.10e+03 1.02e+01 bond pdb=" CA TYR A 418 " pdb=" CB TYR A 418 " ideal model delta sigma weight residual 1.530 1.484 0.046 1.51e-02 4.39e+03 9.44e+00 bond pdb=" CB THR A 140 " pdb=" OG1 THR A 140 " ideal model delta sigma weight residual 1.433 1.385 0.048 1.60e-02 3.91e+03 8.97e+00 ... (remaining 3002 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.88: 2899 1.88 - 3.76: 972 3.76 - 5.63: 183 5.63 - 7.51: 29 7.51 - 9.39: 7 Bond angle restraints: 4090 Sorted by residual: angle pdb=" N MET A 319 " pdb=" CA MET A 319 " pdb=" C MET A 319 " ideal model delta sigma weight residual 111.40 118.41 -7.01 1.22e+00 6.72e-01 3.30e+01 angle pdb=" N VAL A 427 " pdb=" CA VAL A 427 " pdb=" CB VAL A 427 " ideal model delta sigma weight residual 110.54 118.23 -7.69 1.36e+00 5.41e-01 3.20e+01 angle pdb=" N SER A 420 " pdb=" CA SER A 420 " pdb=" C SER A 420 " ideal model delta sigma weight residual 112.04 120.07 -8.03 1.44e+00 4.82e-01 3.11e+01 angle pdb=" CA ILE A 455 " pdb=" C ILE A 455 " pdb=" N ILE A 456 " ideal model delta sigma weight residual 117.28 123.73 -6.45 1.16e+00 7.43e-01 3.09e+01 angle pdb=" CA ASN A 154 " pdb=" CB ASN A 154 " pdb=" CG ASN A 154 " ideal model delta sigma weight residual 112.60 118.14 -5.54 1.00e+00 1.00e+00 3.07e+01 ... (remaining 4085 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.30: 1616 16.30 - 32.60: 141 32.60 - 48.90: 25 48.90 - 65.19: 7 65.19 - 81.49: 1 Dihedral angle restraints: 1790 sinusoidal: 689 harmonic: 1101 Sorted by residual: dihedral pdb=" CA CYS A 360 " pdb=" C CYS A 360 " pdb=" N ALA A 361 " pdb=" CA ALA A 361 " ideal model delta harmonic sigma weight residual 180.00 153.16 26.84 0 5.00e+00 4.00e-02 2.88e+01 dihedral pdb=" CA ILE A 156 " pdb=" C ILE A 156 " pdb=" N GLY A 157 " pdb=" CA GLY A 157 " ideal model delta harmonic sigma weight residual 180.00 -155.51 -24.49 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA ASN A 128 " pdb=" C ASN A 128 " pdb=" N VAL A 129 " pdb=" CA VAL A 129 " ideal model delta harmonic sigma weight residual -180.00 -156.54 -23.46 0 5.00e+00 4.00e-02 2.20e+01 ... (remaining 1787 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 288 0.089 - 0.179: 155 0.179 - 0.268: 34 0.268 - 0.358: 8 0.358 - 0.447: 2 Chirality restraints: 487 Sorted by residual: chirality pdb=" CA SER A 420 " pdb=" N SER A 420 " pdb=" C SER A 420 " pdb=" CB SER A 420 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA LEU A 152 " pdb=" N LEU A 152 " pdb=" C LEU A 152 " pdb=" CB LEU A 152 " both_signs ideal model delta sigma weight residual False 2.51 2.14 0.37 2.00e-01 2.50e+01 3.36e+00 chirality pdb=" CB THR A 140 " pdb=" CA THR A 140 " pdb=" OG1 THR A 140 " pdb=" CG2 THR A 140 " both_signs ideal model delta sigma weight residual False 2.55 2.23 0.32 2.00e-01 2.50e+01 2.55e+00 ... (remaining 484 not shown) Planarity restraints: 501 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 176 " 0.112 2.00e-02 2.50e+03 7.03e-02 8.64e+01 pdb=" CG PHE A 176 " -0.068 2.00e-02 2.50e+03 pdb=" CD1 PHE A 176 " -0.075 2.00e-02 2.50e+03 pdb=" CD2 PHE A 176 " -0.072 2.00e-02 2.50e+03 pdb=" CE1 PHE A 176 " 0.015 2.00e-02 2.50e+03 pdb=" CE2 PHE A 176 " 0.009 2.00e-02 2.50e+03 pdb=" CZ PHE A 176 " 0.079 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C05 EBZ A 601 " -0.062 2.00e-02 2.50e+03 5.00e-02 6.24e+01 pdb=" C06 EBZ A 601 " -0.039 2.00e-02 2.50e+03 pdb=" C07 EBZ A 601 " -0.019 2.00e-02 2.50e+03 pdb=" C09 EBZ A 601 " 0.017 2.00e-02 2.50e+03 pdb=" C14 EBZ A 601 " 0.098 2.00e-02 2.50e+03 pdb=" C15 EBZ A 601 " 0.028 2.00e-02 2.50e+03 pdb=" C16 EBZ A 601 " -0.010 2.00e-02 2.50e+03 pdb=" C17 EBZ A 601 " -0.015 2.00e-02 2.50e+03 pdb=" O01 EBZ A 601 " 0.065 2.00e-02 2.50e+03 pdb=" O02 EBZ A 601 " -0.063 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 422 " 0.091 2.00e-02 2.50e+03 4.75e-02 4.51e+01 pdb=" CG TYR A 422 " -0.041 2.00e-02 2.50e+03 pdb=" CD1 TYR A 422 " -0.031 2.00e-02 2.50e+03 pdb=" CD2 TYR A 422 " -0.050 2.00e-02 2.50e+03 pdb=" CE1 TYR A 422 " -0.024 2.00e-02 2.50e+03 pdb=" CE2 TYR A 422 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 422 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR A 422 " 0.064 2.00e-02 2.50e+03 ... (remaining 498 not shown) Histogram of nonbonded interaction distances: 2.54 - 3.01: 1517 3.01 - 3.48: 3458 3.48 - 3.95: 4867 3.95 - 4.43: 5561 4.43 - 4.90: 9114 Nonbonded interactions: 24517 Sorted by model distance: nonbonded pdb=" OD1 ASP A 411 " pdb=" OH TYR A 418 " model vdw 2.537 3.040 nonbonded pdb=" O SER A 420 " pdb=" N ALA A 423 " model vdw 2.561 3.120 nonbonded pdb=" N THR A 249 " pdb=" N ALA A 250 " model vdw 2.562 2.560 nonbonded pdb=" O ILE A 455 " pdb=" CA ILE A 456 " model vdw 2.574 2.776 nonbonded pdb=" OD1 ASP A 411 " pdb=" OG SER A 416 " model vdw 2.601 3.040 ... (remaining 24512 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: 2.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.070 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7194 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 : 0.012 0.049 3007 Z= 0.790 Angle : 1.889 9.388 4090 Z= 1.258 Chirality : 0.108 0.447 487 Planarity : 0.014 0.070 501 Dihedral : 13.084 81.492 1088 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.96 % Allowed : 7.03 % Favored : 92.01 % Cbeta Deviations : 0.28 % 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: -3.14 (0.37), residues: 385 helix: -1.94 (0.25), residues: 275 sheet: None (None), residues: 0 loop : -1.95 (0.61), residues: 110 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.070 0.016 TRP A 451 HIS 0.003 0.002 HIS A 353 PHE 0.112 0.016 PHE A 176 TYR 0.091 0.015 TYR A 422 ARG 0.004 0.001 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.304 Fit side-chains revert: symmetry clash REVERT: A 443 ILE cc_start: 0.7773 (mt) cc_final: 0.7455 (mt) outliers start: 3 outliers final: 0 residues processed: 83 average time/residue: 0.0998 time to fit residues: 10.8304 Evaluate side-chains 67 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 67 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 18 optimal weight: 0.0050 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 34 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 128 ASN A 154 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4029 r_free = 0.4029 target = 0.141388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3903 r_free = 0.3903 target = 0.130371 restraints weight = 4956.420| |-----------------------------------------------------------------------------| r_work (start): 0.3919 rms_B_bonded: 2.17 r_work: 0.3819 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7022 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3007 Z= 0.313 Angle : 0.833 7.904 4090 Z= 0.415 Chirality : 0.048 0.173 487 Planarity : 0.006 0.058 501 Dihedral : 7.437 25.941 441 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.56 % Allowed : 14.38 % Favored : 83.07 % 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: -1.14 (0.43), residues: 385 helix: -0.37 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.48 (0.70), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 328 HIS 0.001 0.001 HIS A 414 PHE 0.019 0.002 PHE A 238 TYR 0.014 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 70 time to evaluate : 0.310 Fit side-chains REVERT: A 244 GLU cc_start: 0.7055 (OUTLIER) cc_final: 0.6647 (tt0) REVERT: A 443 ILE cc_start: 0.7706 (mt) cc_final: 0.7351 (mt) outliers start: 8 outliers final: 2 residues processed: 75 average time/residue: 0.0968 time to fit residues: 9.5896 Evaluate side-chains 68 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 65 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 244 GLU Chi-restraints excluded: chain A residue 283 THR Chi-restraints excluded: chain A residue 339 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 0.0980 chunk 35 optimal weight: 0.6980 chunk 34 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 28 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 0.6980 chunk 9 optimal weight: 0.2980 chunk 16 optimal weight: 0.6980 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4070 r_free = 0.4070 target = 0.144750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.133494 restraints weight = 5037.501| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.25 r_work: 0.3854 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3854 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6993 moved from start: 0.2720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3007 Z= 0.242 Angle : 0.766 9.402 4090 Z= 0.374 Chirality : 0.046 0.151 487 Planarity : 0.006 0.060 501 Dihedral : 6.911 25.665 441 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.24 % Allowed : 17.57 % Favored : 80.19 % 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 (0.43), residues: 385 helix: -0.04 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -1.53 (0.67), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 328 HIS 0.002 0.001 HIS A 414 PHE 0.014 0.002 PHE A 238 TYR 0.020 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 68 time to evaluate : 0.286 Fit side-chains REVERT: A 244 GLU cc_start: 0.6943 (tt0) cc_final: 0.6734 (tt0) REVERT: A 443 ILE cc_start: 0.7600 (mt) cc_final: 0.7295 (mt) outliers start: 7 outliers final: 2 residues processed: 71 average time/residue: 0.0986 time to fit residues: 9.2220 Evaluate side-chains 66 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 283 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 16 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4035 r_free = 0.4035 target = 0.141471 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.130371 restraints weight = 5004.874| |-----------------------------------------------------------------------------| r_work (start): 0.3900 rms_B_bonded: 2.22 r_work: 0.3808 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3678 rms_B_bonded: 4.95 restraints_weight: 0.2500 r_work (final): 0.3678 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.2958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 3007 Z= 0.337 Angle : 0.808 7.461 4090 Z= 0.393 Chirality : 0.048 0.159 487 Planarity : 0.006 0.065 501 Dihedral : 6.835 24.018 441 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 10.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.24 % Allowed : 21.09 % Favored : 76.68 % 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: -0.84 (0.42), residues: 385 helix: -0.08 (0.30), residues: 283 sheet: None (None), residues: 0 loop : -1.64 (0.67), residues: 102 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 328 HIS 0.004 0.001 HIS A 414 PHE 0.014 0.002 PHE A 178 TYR 0.021 0.003 TYR A 422 ARG 0.001 0.000 ARG A 413 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.314 Fit side-chains REVERT: A 323 MET cc_start: 0.6174 (ppp) cc_final: 0.5692 (ppp) REVERT: A 355 MET cc_start: 0.7120 (ptp) cc_final: 0.6865 (ptp) REVERT: A 443 ILE cc_start: 0.7840 (mt) cc_final: 0.7507 (mt) outliers start: 7 outliers final: 5 residues processed: 68 average time/residue: 0.1061 time to fit residues: 9.4773 Evaluate side-chains 68 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.9990 chunk 15 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 22 optimal weight: 0.1980 chunk 5 optimal weight: 0.0870 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.0980 chunk 17 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 overall best weight: 0.3158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4093 r_free = 0.4093 target = 0.145659 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.134463 restraints weight = 5036.945| |-----------------------------------------------------------------------------| r_work (start): 0.3947 rms_B_bonded: 2.27 r_work: 0.3855 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work (final): 0.3855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6982 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 3007 Z= 0.228 Angle : 0.734 8.634 4090 Z= 0.354 Chirality : 0.044 0.145 487 Planarity : 0.006 0.064 501 Dihedral : 6.517 23.926 441 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 2.88 % Allowed : 19.49 % 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: -0.50 (0.43), residues: 385 helix: 0.30 (0.31), residues: 279 sheet: None (None), residues: 0 loop : -1.88 (0.63), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 451 HIS 0.002 0.001 HIS A 414 PHE 0.011 0.001 PHE A 238 TYR 0.017 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.287 Fit side-chains REVERT: A 185 LEU cc_start: 0.5447 (tp) cc_final: 0.5169 (tp) REVERT: A 405 ILE cc_start: 0.6768 (OUTLIER) cc_final: 0.6332 (mm) REVERT: A 443 ILE cc_start: 0.7711 (mt) cc_final: 0.7383 (mt) outliers start: 9 outliers final: 6 residues processed: 68 average time/residue: 0.1017 time to fit residues: 9.2168 Evaluate side-chains 69 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 62 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 306 MET Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 4 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.0070 chunk 9 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.143490 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3929 r_free = 0.3929 target = 0.131993 restraints weight = 5103.227| |-----------------------------------------------------------------------------| r_work (start): 0.3920 rms_B_bonded: 2.29 r_work: 0.3823 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.3317 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 3007 Z= 0.294 Angle : 0.768 8.041 4090 Z= 0.372 Chirality : 0.046 0.166 487 Planarity : 0.006 0.065 501 Dihedral : 6.621 23.452 441 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.19 % Allowed : 20.77 % Favored : 76.04 % 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: -0.62 (0.43), residues: 385 helix: 0.22 (0.31), residues: 279 sheet: None (None), residues: 0 loop : -1.94 (0.61), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.011 0.002 PHE A 178 TYR 0.020 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.282 Fit side-chains REVERT: A 185 LEU cc_start: 0.5580 (tp) cc_final: 0.5285 (tp) REVERT: A 405 ILE cc_start: 0.6849 (OUTLIER) cc_final: 0.6450 (mm) outliers start: 10 outliers final: 8 residues processed: 72 average time/residue: 0.0978 time to fit residues: 9.3115 Evaluate side-chains 72 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 63 time to evaluate : 0.283 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 366 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.0980 chunk 13 optimal weight: 0.9980 chunk 32 optimal weight: 0.2980 chunk 24 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.4980 chunk 8 optimal weight: 0.1980 chunk 23 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 0 optimal weight: 0.9980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 192 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4092 r_free = 0.4092 target = 0.145524 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.135329 restraints weight = 4939.171| |-----------------------------------------------------------------------------| r_work (start): 0.3960 rms_B_bonded: 2.08 r_work: 0.3864 rms_B_bonded: 2.70 restraints_weight: 0.5000 r_work: 0.3734 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3734 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7095 moved from start: 0.3538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3007 Z= 0.235 Angle : 0.759 9.237 4090 Z= 0.361 Chirality : 0.044 0.179 487 Planarity : 0.006 0.063 501 Dihedral : 6.493 23.415 441 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 10.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.51 % Allowed : 20.77 % Favored : 75.72 % 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: -0.46 (0.43), residues: 385 helix: 0.32 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.91 (0.62), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.024 0.002 PHE A 429 TYR 0.017 0.002 TYR A 422 ARG 0.002 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.419 Fit side-chains REVERT: A 185 LEU cc_start: 0.5509 (tp) cc_final: 0.5204 (tp) REVERT: A 405 ILE cc_start: 0.7004 (OUTLIER) cc_final: 0.6527 (mm) outliers start: 11 outliers final: 7 residues processed: 73 average time/residue: 0.1002 time to fit residues: 9.7585 Evaluate side-chains 74 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 66 time to evaluate : 0.265 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 8 optimal weight: 0.0980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 9 optimal weight: 0.0970 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4066 r_free = 0.4066 target = 0.143205 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.132397 restraints weight = 4914.358| |-----------------------------------------------------------------------------| r_work (start): 0.3942 rms_B_bonded: 2.19 r_work: 0.3844 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3007 Z= 0.264 Angle : 0.782 10.189 4090 Z= 0.372 Chirality : 0.045 0.179 487 Planarity : 0.006 0.064 501 Dihedral : 6.504 23.346 441 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 4.47 % Allowed : 20.77 % Favored : 74.76 % 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: -0.47 (0.43), residues: 385 helix: 0.31 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.89 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.003 0.001 HIS A 414 PHE 0.021 0.002 PHE A 429 TYR 0.019 0.002 TYR A 422 ARG 0.001 0.000 ARG A 189 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.352 Fit side-chains REVERT: A 185 LEU cc_start: 0.5462 (tp) cc_final: 0.5189 (tp) REVERT: A 355 MET cc_start: 0.6696 (ptp) cc_final: 0.6395 (ptp) REVERT: A 405 ILE cc_start: 0.6813 (OUTLIER) cc_final: 0.6403 (mm) REVERT: A 406 MET cc_start: 0.6895 (mpp) cc_final: 0.6560 (mpp) outliers start: 14 outliers final: 10 residues processed: 77 average time/residue: 0.0999 time to fit residues: 10.2212 Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 137 SER Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 13 optimal weight: 0.9980 chunk 31 optimal weight: 0.1980 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 2 optimal weight: 0.0870 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 1 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.143731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3942 r_free = 0.3942 target = 0.132850 restraints weight = 4886.002| |-----------------------------------------------------------------------------| r_work (start): 0.3949 rms_B_bonded: 2.20 r_work: 0.3852 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3852 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.3696 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3007 Z= 0.249 Angle : 0.802 11.103 4090 Z= 0.375 Chirality : 0.046 0.193 487 Planarity : 0.006 0.063 501 Dihedral : 6.490 23.355 441 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 11.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.83 % Allowed : 21.73 % Favored : 74.44 % 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: -0.36 (0.43), residues: 385 helix: 0.38 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.81 (0.64), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.026 0.002 PHE A 348 TYR 0.026 0.002 TYR A 243 ARG 0.001 0.000 ARG A 326 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 70 time to evaluate : 0.304 Fit side-chains REVERT: A 185 LEU cc_start: 0.5473 (tp) cc_final: 0.5195 (tp) REVERT: A 355 MET cc_start: 0.6702 (ptp) cc_final: 0.6468 (ptp) REVERT: A 405 ILE cc_start: 0.6821 (OUTLIER) cc_final: 0.6405 (mm) outliers start: 12 outliers final: 9 residues processed: 77 average time/residue: 0.0999 time to fit residues: 10.1161 Evaluate side-chains 79 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 3 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 15 optimal weight: 0.1980 chunk 26 optimal weight: 0.8980 chunk 28 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 23 optimal weight: 0.4980 chunk 13 optimal weight: 0.7980 chunk 20 optimal weight: 0.0670 chunk 7 optimal weight: 0.4980 overall best weight: 0.3718 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4077 r_free = 0.4077 target = 0.144285 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.133746 restraints weight = 4889.725| |-----------------------------------------------------------------------------| r_work (start): 0.3964 rms_B_bonded: 2.16 r_work: 0.3865 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work (final): 0.3865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6987 moved from start: 0.3789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3007 Z= 0.245 Angle : 0.808 11.300 4090 Z= 0.376 Chirality : 0.045 0.198 487 Planarity : 0.006 0.063 501 Dihedral : 6.468 23.422 441 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 12.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.19 % Allowed : 22.36 % Favored : 74.44 % 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: -0.29 (0.44), residues: 385 helix: 0.44 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.79 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 318 HIS 0.002 0.001 HIS A 414 PHE 0.024 0.002 PHE A 348 TYR 0.024 0.002 TYR A 243 ARG 0.001 0.000 ARG A 189 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 770 Ramachandran restraints generated. 385 Oldfield, 0 Emsley, 385 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.306 Fit side-chains REVERT: A 185 LEU cc_start: 0.5478 (tp) cc_final: 0.5212 (tp) REVERT: A 405 ILE cc_start: 0.6871 (OUTLIER) cc_final: 0.6458 (mm) REVERT: A 406 MET cc_start: 0.6902 (mpp) cc_final: 0.6565 (mpp) outliers start: 10 outliers final: 9 residues processed: 73 average time/residue: 0.1021 time to fit residues: 9.7895 Evaluate side-chains 79 residues out of total 314 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 ASN Chi-restraints excluded: chain A residue 149 ILE Chi-restraints excluded: chain A residue 245 PHE Chi-restraints excluded: chain A residue 249 THR Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 280 GLN Chi-restraints excluded: chain A residue 339 ILE Chi-restraints excluded: chain A residue 350 ILE Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 405 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 7 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 6 optimal weight: 0.3980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 23 optimal weight: 0.3980 overall best weight: 0.4158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4079 r_free = 0.4079 target = 0.144236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 21)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.133363 restraints weight = 4920.863| |-----------------------------------------------------------------------------| r_work (start): 0.3959 rms_B_bonded: 2.21 r_work: 0.3860 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work (final): 0.3860 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.3793 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3007 Z= 0.261 Angle : 0.827 11.523 4090 Z= 0.384 Chirality : 0.046 0.190 487 Planarity : 0.006 0.063 501 Dihedral : 6.467 23.146 441 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 12.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 3.51 % Allowed : 22.36 % Favored : 74.12 % 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: -0.30 (0.43), residues: 385 helix: 0.41 (0.31), residues: 282 sheet: None (None), residues: 0 loop : -1.75 (0.63), residues: 103 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 328 HIS 0.003 0.001 HIS A 414 PHE 0.024 0.002 PHE A 348 TYR 0.023 0.002 TYR A 243 ARG 0.001 0.000 ARG A 189 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1816.56 seconds wall clock time: 32 minutes 11.89 seconds (1931.89 seconds total)