Starting phenix.real_space_refine on Wed Mar 5 18:46:16 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8cud_26998/03_2025/8cud_26998.cif Found real_map, /net/cci-nas-00/data/ceres_data/8cud_26998/03_2025/8cud_26998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.94 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8cud_26998/03_2025/8cud_26998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8cud_26998/03_2025/8cud_26998.map" model { file = "/net/cci-nas-00/data/ceres_data/8cud_26998/03_2025/8cud_26998.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8cud_26998/03_2025/8cud_26998.cif" } resolution = 2.94 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.004 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 21 5.16 5 C 2153 2.51 5 N 526 2.21 5 O 594 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3294 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3292 Number of conformers: 1 Conformer: "" Number of residues, atoms: 433, 3292 Classifications: {'peptide': 433} Link IDs: {'PTRANS': 12, 'TRANS': 420} Chain breaks: 1 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Classifications: {'water': 2} Link IDs: {None: 1} Time building chain proxies: 2.71, per 1000 atoms: 0.82 Number of scatterers: 3294 At special positions: 0 Unit cell: (71.568, 66.456, 80.088, 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 21 16.00 O 594 8.00 N 526 7.00 C 2153 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: 0.79 Conformation dependent library (CDL) restraints added in 377.9 milliseconds 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 800 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 1 sheets defined 81.5% alpha, 3.2% 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 19 through 42 removed outlier: 3.604A pdb=" N ILE A 32 " --> pdb=" O VAL A 28 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N THR A 33 " --> pdb=" O VAL A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 52 removed outlier: 3.520A pdb=" N PHE A 52 " --> pdb=" O GLU A 48 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 64 Processing helix chain 'A' and resid 66 through 82 removed outlier: 3.888A pdb=" N LEU A 82 " --> pdb=" O GLY A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 117 removed outlier: 3.673A pdb=" N GLY A 88 " --> pdb=" O SER A 84 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LYS A 89 " --> pdb=" O ASN A 85 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 150 removed outlier: 3.551A pdb=" N LEU A 145 " --> pdb=" O ALA A 141 " (cutoff:3.500A) removed outlier: 3.970A pdb=" N ILE A 146 " --> pdb=" O MET A 142 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N PHE A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) Processing helix chain 'A' and resid 155 through 158 Processing helix chain 'A' and resid 211 through 228 removed outlier: 3.659A pdb=" N LYS A 228 " --> pdb=" O LEU A 224 " (cutoff:3.500A) Processing helix chain 'A' and resid 229 through 232 removed outlier: 3.616A pdb=" N LYS A 232 " --> pdb=" O MET A 229 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 229 through 232' Processing helix chain 'A' and resid 233 through 270 removed outlier: 3.596A pdb=" N VAL A 251 " --> pdb=" O THR A 247 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N GLN A 252 " --> pdb=" O MET A 248 " (cutoff:3.500A) removed outlier: 4.111A pdb=" N ILE A 253 " --> pdb=" O LYS A 249 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N TRP A 256 " --> pdb=" O GLN A 252 " (cutoff:3.500A) removed outlier: 3.940A pdb=" N TYR A 257 " --> pdb=" O ILE A 253 " (cutoff:3.500A) Proline residue: A 259 - end of helix removed outlier: 3.644A pdb=" N GLY A 268 " --> pdb=" O PHE A 264 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N CYS A 269 " --> pdb=" O LEU A 265 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ILE A 270 " --> pdb=" O ILE A 266 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 282 Processing helix chain 'A' and resid 282 through 299 Processing helix chain 'A' and resid 299 through 309 Processing helix chain 'A' and resid 312 through 319 removed outlier: 4.157A pdb=" N PHE A 316 " --> pdb=" O ASN A 312 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 331 Processing helix chain 'A' and resid 336 through 348 removed outlier: 3.517A pdb=" N ASN A 348 " --> pdb=" O ALA A 344 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 366 removed outlier: 4.179A pdb=" N PHE A 357 " --> pdb=" O ARG A 353 " (cutoff:3.500A) Proline residue: A 360 - end of helix removed outlier: 4.032A pdb=" N THR A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 385 Processing helix chain 'A' and resid 390 through 408 removed outlier: 3.796A pdb=" N ILE A 406 " --> pdb=" O THR A 402 " (cutoff:3.500A) Processing helix chain 'A' and resid 413 through 427 removed outlier: 3.648A pdb=" N VAL A 417 " --> pdb=" O GLN A 413 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 432 removed outlier: 3.678A pdb=" N ASP A 432 " --> pdb=" O PRO A 429 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 429 through 432' Processing helix chain 'A' and resid 433 through 438 removed outlier: 3.623A pdb=" N ILE A 437 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 4.308A pdb=" N ALA A 438 " --> pdb=" O THR A 434 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 433 through 438' Processing helix chain 'A' and resid 442 through 466 removed outlier: 3.802A pdb=" N PHE A 446 " --> pdb=" O LEU A 442 " (cutoff:3.500A) removed outlier: 3.604A pdb=" N ARG A 447 " --> pdb=" O LEU A 443 " (cutoff:3.500A) removed outlier: 4.020A pdb=" N THR A 448 " --> pdb=" O ASP A 444 " (cutoff:3.500A) removed outlier: 4.159A pdb=" N MET A 449 " --> pdb=" O ARG A 445 " (cutoff:3.500A) removed outlier: 3.832A pdb=" N VAL A 450 " --> pdb=" O PHE A 446 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 473 Processing sheet with id=AA1, first strand: chain 'A' and resid 160 through 167 229 hydrogen bonds defined for protein. 681 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: 0.82 Time building geometry restraints manager: 0.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 936 1.34 - 1.45: 415 1.45 - 1.57: 1951 1.57 - 1.69: 0 1.69 - 1.81: 39 Bond restraints: 3341 Sorted by residual: bond pdb=" N VAL A 113 " pdb=" CA VAL A 113 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.47e+00 bond pdb=" N MET A 367 " pdb=" CA MET A 367 " ideal model delta sigma weight residual 1.458 1.493 -0.035 1.14e-02 7.69e+03 9.37e+00 bond pdb=" N ILE A 210 " pdb=" CA ILE A 210 " ideal model delta sigma weight residual 1.458 1.496 -0.039 1.27e-02 6.20e+03 9.33e+00 bond pdb=" N ILE A 116 " pdb=" CA ILE A 116 " ideal model delta sigma weight residual 1.461 1.497 -0.036 1.19e-02 7.06e+03 9.16e+00 bond pdb=" N ILE A 365 " pdb=" CA ILE A 365 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 8.98e+00 ... (remaining 3336 not shown) Histogram of bond angle deviations from ideal: 0.00 - 0.99: 4143 0.99 - 1.98: 248 1.98 - 2.97: 106 2.97 - 3.96: 27 3.96 - 4.95: 12 Bond angle restraints: 4536 Sorted by residual: angle pdb=" CA ASP A 368 " pdb=" C ASP A 368 " pdb=" O ASP A 368 " ideal model delta sigma weight residual 121.07 116.89 4.18 1.10e+00 8.26e-01 1.44e+01 angle pdb=" CA ILE A 116 " pdb=" C ILE A 116 " pdb=" O ILE A 116 " ideal model delta sigma weight residual 120.95 117.14 3.81 1.04e+00 9.25e-01 1.34e+01 angle pdb=" CA THR A 448 " pdb=" C THR A 448 " pdb=" O THR A 448 " ideal model delta sigma weight residual 120.82 117.18 3.64 1.05e+00 9.07e-01 1.21e+01 angle pdb=" N ARG A 315 " pdb=" CA ARG A 315 " pdb=" C ARG A 315 " ideal model delta sigma weight residual 111.36 107.59 3.77 1.09e+00 8.42e-01 1.20e+01 angle pdb=" C GLY A 369 " pdb=" N THR A 370 " pdb=" CA THR A 370 " ideal model delta sigma weight residual 120.54 125.06 -4.52 1.35e+00 5.49e-01 1.12e+01 ... (remaining 4531 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.91: 1765 17.91 - 35.83: 182 35.83 - 53.74: 44 53.74 - 71.65: 6 71.65 - 89.57: 4 Dihedral angle restraints: 2001 sinusoidal: 760 harmonic: 1241 Sorted by residual: dihedral pdb=" CA GLU A 40 " pdb=" C GLU A 40 " pdb=" N HIS A 41 " pdb=" CA HIS A 41 " ideal model delta harmonic sigma weight residual 180.00 -163.09 -16.91 0 5.00e+00 4.00e-02 1.14e+01 dihedral pdb=" CB GLU A 463 " pdb=" CG GLU A 463 " pdb=" CD GLU A 463 " pdb=" OE1 GLU A 463 " ideal model delta sinusoidal sigma weight residual 0.00 -89.57 89.57 1 3.00e+01 1.11e-03 1.06e+01 dihedral pdb=" C ASP A 368 " pdb=" N ASP A 368 " pdb=" CA ASP A 368 " pdb=" CB ASP A 368 " ideal model delta harmonic sigma weight residual -122.60 -130.60 8.00 0 2.50e+00 1.60e-01 1.03e+01 ... (remaining 1998 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 405 0.042 - 0.083: 111 0.083 - 0.125: 40 0.125 - 0.166: 14 0.166 - 0.208: 5 Chirality restraints: 575 Sorted by residual: chirality pdb=" CA ASP A 368 " pdb=" N ASP A 368 " pdb=" C ASP A 368 " pdb=" CB ASP A 368 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CB VAL A 113 " pdb=" CA VAL A 113 " pdb=" CG1 VAL A 113 " pdb=" CG2 VAL A 113 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA MET A 318 " pdb=" N MET A 318 " pdb=" C MET A 318 " pdb=" CB MET A 318 " both_signs ideal model delta sigma weight residual False 2.51 2.68 -0.17 2.00e-01 2.50e+01 7.38e-01 ... (remaining 572 not shown) Planarity restraints: 555 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR A 364 " -0.010 2.00e-02 2.50e+03 2.05e-02 4.21e+00 pdb=" C THR A 364 " 0.035 2.00e-02 2.50e+03 pdb=" O THR A 364 " -0.013 2.00e-02 2.50e+03 pdb=" N ILE A 365 " -0.012 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 411 " 0.021 5.00e-02 4.00e+02 3.21e-02 1.65e+00 pdb=" N PRO A 412 " -0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " 0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 66 " 0.006 2.00e-02 2.50e+03 1.15e-02 1.31e+00 pdb=" C ILE A 66 " -0.020 2.00e-02 2.50e+03 pdb=" O ILE A 66 " 0.007 2.00e-02 2.50e+03 pdb=" N ILE A 67 " 0.007 2.00e-02 2.50e+03 ... (remaining 552 not shown) Histogram of nonbonded interaction distances: 2.43 - 2.93: 1340 2.93 - 3.42: 3473 3.42 - 3.91: 5224 3.91 - 4.41: 5551 4.41 - 4.90: 9805 Nonbonded interactions: 25393 Sorted by model distance: nonbonded pdb=" O PRO A 69 " pdb=" OG SER A 73 " model vdw 2.433 3.040 nonbonded pdb=" OE2 GLU A 345 " pdb=" NH1 ARG A 356 " model vdw 2.437 3.120 nonbonded pdb=" O SER A 331 " pdb=" OG SER A 331 " model vdw 2.535 3.040 nonbonded pdb=" OD1 ASN A 312 " pdb=" N PHE A 314 " model vdw 2.547 3.120 nonbonded pdb=" OH TYR A 373 " pdb=" OD1 ASP A 440 " model vdw 2.554 3.040 ... (remaining 25388 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: 1.060 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: 12.520 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:10.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8027 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.072 3341 Z= 0.294 Angle : 0.667 4.948 4536 Z= 0.466 Chirality : 0.049 0.208 575 Planarity : 0.004 0.032 555 Dihedral : 15.611 89.566 1201 Min Nonbonded Distance : 2.433 Molprobity Statistics. All-atom Clashscore : 3.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 0.00 % Allowed : 22.99 % Favored : 77.01 % 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: 1.42 (0.42), residues: 429 helix: 1.51 (0.31), residues: 320 sheet: 1.60 (1.19), residues: 16 loop : -1.08 (0.56), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 19 HIS 0.002 0.001 HIS A 41 PHE 0.011 0.001 PHE A 457 TYR 0.010 0.001 TYR A 97 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.403 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 58 average time/residue: 1.0924 time to fit residues: 65.4247 Evaluate side-chains 47 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 6.9990 chunk 32 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.0570 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 overall best weight: 0.8100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 366 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.177172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.128326 restraints weight = 3867.770| |-----------------------------------------------------------------------------| r_work (start): 0.3375 rms_B_bonded: 1.74 r_work: 0.3240 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3128 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8092 moved from start: 0.1182 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3341 Z= 0.171 Angle : 0.482 5.429 4536 Z= 0.255 Chirality : 0.038 0.136 575 Planarity : 0.004 0.030 555 Dihedral : 3.486 14.402 455 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 3.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.60 % Allowed : 22.44 % Favored : 73.96 % 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: 1.80 (0.42), residues: 429 helix: 1.91 (0.31), residues: 321 sheet: 1.97 (1.23), residues: 16 loop : -1.61 (0.57), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.010 0.001 TYR A 373 ARG 0.004 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 51 time to evaluate : 0.354 Fit side-chains REVERT: A 231 GLU cc_start: 0.7516 (OUTLIER) cc_final: 0.7183 (tp30) REVERT: A 367 MET cc_start: 0.7624 (mmt) cc_final: 0.7406 (mmp) REVERT: A 428 LEU cc_start: 0.6955 (OUTLIER) cc_final: 0.6680 (mt) outliers start: 13 outliers final: 3 residues processed: 60 average time/residue: 0.9654 time to fit residues: 60.0986 Evaluate side-chains 50 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 34 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 36 optimal weight: 20.0000 chunk 31 optimal weight: 1.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 348 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 = 0.3993 r_free = 0.3993 target = 0.176220 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.127003 restraints weight = 3789.421| |-----------------------------------------------------------------------------| r_work (start): 0.3356 rms_B_bonded: 1.76 r_work: 0.3218 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3104 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3104 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8115 moved from start: 0.1451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3341 Z= 0.176 Angle : 0.477 5.749 4536 Z= 0.250 Chirality : 0.039 0.201 575 Planarity : 0.003 0.031 555 Dihedral : 3.432 14.394 455 Min Nonbonded Distance : 2.640 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 4.99 % Allowed : 21.33 % Favored : 73.68 % 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: 1.73 (0.42), residues: 429 helix: 1.99 (0.31), residues: 314 sheet: 1.99 (1.18), residues: 16 loop : -1.89 (0.56), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.010 0.001 TYR A 373 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 47 time to evaluate : 0.296 Fit side-chains REVERT: A 200 TYR cc_start: 0.8105 (m-10) cc_final: 0.7716 (m-10) REVERT: A 428 LEU cc_start: 0.6928 (OUTLIER) cc_final: 0.6585 (mp) outliers start: 18 outliers final: 5 residues processed: 60 average time/residue: 0.8738 time to fit residues: 54.4818 Evaluate side-chains 49 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 31 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 26 optimal weight: 0.4980 chunk 23 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 24 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.176778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.127630 restraints weight = 3886.826| |-----------------------------------------------------------------------------| r_work (start): 0.3365 rms_B_bonded: 1.76 r_work: 0.3227 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3115 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.3115 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1573 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3341 Z= 0.159 Angle : 0.473 7.034 4536 Z= 0.247 Chirality : 0.039 0.177 575 Planarity : 0.003 0.040 555 Dihedral : 3.394 14.598 455 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 5.26 % Allowed : 21.05 % Favored : 73.68 % 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: 1.93 (0.42), residues: 429 helix: 1.99 (0.30), residues: 321 sheet: 2.24 (1.27), residues: 16 loop : -1.55 (0.57), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.012 0.001 PHE A 341 TYR 0.013 0.001 TYR A 373 ARG 0.003 0.000 ARG A 356 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.370 Fit side-chains REVERT: A 200 TYR cc_start: 0.8097 (m-10) cc_final: 0.7705 (m-10) REVERT: A 231 GLU cc_start: 0.7476 (OUTLIER) cc_final: 0.7150 (tp30) REVERT: A 428 LEU cc_start: 0.6895 (OUTLIER) cc_final: 0.6550 (mp) outliers start: 19 outliers final: 7 residues processed: 60 average time/residue: 0.9684 time to fit residues: 60.3220 Evaluate side-chains 51 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.321 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 14 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 18 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176604 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.127469 restraints weight = 3840.883| |-----------------------------------------------------------------------------| r_work (start): 0.3363 rms_B_bonded: 1.76 r_work: 0.3229 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.3114 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3114 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8098 moved from start: 0.1645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3341 Z= 0.159 Angle : 0.471 5.404 4536 Z= 0.246 Chirality : 0.039 0.226 575 Planarity : 0.003 0.045 555 Dihedral : 3.382 14.032 455 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 5.26 % Allowed : 21.05 % Favored : 73.68 % 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: 1.85 (0.42), residues: 429 helix: 2.00 (0.31), residues: 317 sheet: 2.44 (1.34), residues: 16 loop : -1.74 (0.56), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.012 0.001 PHE A 341 TYR 0.012 0.001 TYR A 373 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 45 time to evaluate : 0.371 Fit side-chains REVERT: A 200 TYR cc_start: 0.8103 (m-10) cc_final: 0.7706 (m-10) REVERT: A 231 GLU cc_start: 0.7473 (OUTLIER) cc_final: 0.7128 (tp30) REVERT: A 311 LYS cc_start: 0.7268 (OUTLIER) cc_final: 0.6779 (ttmt) REVERT: A 428 LEU cc_start: 0.6892 (OUTLIER) cc_final: 0.6536 (mp) outliers start: 19 outliers final: 9 residues processed: 59 average time/residue: 1.0352 time to fit residues: 63.2757 Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 21 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN ** A 348 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3994 r_free = 0.3994 target = 0.176208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.127009 restraints weight = 3966.523| |-----------------------------------------------------------------------------| r_work (start): 0.3358 rms_B_bonded: 1.78 r_work: 0.3220 rms_B_bonded: 2.61 restraints_weight: 0.5000 r_work: 0.3107 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3107 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3341 Z= 0.165 Angle : 0.471 5.367 4536 Z= 0.247 Chirality : 0.039 0.172 575 Planarity : 0.004 0.048 555 Dihedral : 3.402 14.001 455 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 5.26 % Allowed : 21.61 % Favored : 73.13 % 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: 1.84 (0.42), residues: 429 helix: 2.00 (0.31), residues: 317 sheet: 2.52 (1.43), residues: 16 loop : -1.81 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.000 HIS A 296 PHE 0.012 0.001 PHE A 341 TYR 0.015 0.001 TYR A 373 ARG 0.002 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 46 time to evaluate : 0.330 Fit side-chains REVERT: A 200 TYR cc_start: 0.8122 (m-10) cc_final: 0.7718 (m-10) REVERT: A 231 GLU cc_start: 0.7509 (OUTLIER) cc_final: 0.7187 (tp30) REVERT: A 311 LYS cc_start: 0.7242 (OUTLIER) cc_final: 0.6735 (ttmt) REVERT: A 428 LEU cc_start: 0.6855 (OUTLIER) cc_final: 0.6482 (mp) outliers start: 19 outliers final: 10 residues processed: 59 average time/residue: 0.9459 time to fit residues: 57.9125 Evaluate side-chains 57 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 44 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 307 ILE Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 4.9990 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 0 optimal weight: 8.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.172582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.120983 restraints weight = 3875.023| |-----------------------------------------------------------------------------| r_work (start): 0.3317 rms_B_bonded: 1.84 r_work: 0.3173 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.33 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3341 Z= 0.239 Angle : 0.527 6.490 4536 Z= 0.276 Chirality : 0.042 0.319 575 Planarity : 0.004 0.051 555 Dihedral : 3.606 15.062 455 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 4.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.43 % Allowed : 23.55 % Favored : 72.02 % 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: 1.57 (0.42), residues: 429 helix: 1.82 (0.30), residues: 317 sheet: 2.35 (1.47), residues: 16 loop : -1.92 (0.54), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 256 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.002 PHE A 341 TYR 0.016 0.002 TYR A 373 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 46 time to evaluate : 0.394 Fit side-chains REVERT: A 200 TYR cc_start: 0.8183 (m-10) cc_final: 0.7790 (m-10) REVERT: A 231 GLU cc_start: 0.7696 (OUTLIER) cc_final: 0.7474 (tp30) REVERT: A 311 LYS cc_start: 0.7249 (OUTLIER) cc_final: 0.6775 (ttmt) REVERT: A 428 LEU cc_start: 0.6861 (OUTLIER) cc_final: 0.6502 (mp) outliers start: 16 outliers final: 6 residues processed: 56 average time/residue: 0.9713 time to fit residues: 56.4838 Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 231 GLU Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.174316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3431 r_free = 0.3431 target = 0.126799 restraints weight = 3849.081| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 2.01 r_work: 0.3167 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3053 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1843 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3341 Z= 0.230 Angle : 0.519 6.394 4536 Z= 0.273 Chirality : 0.041 0.253 575 Planarity : 0.004 0.051 555 Dihedral : 3.640 15.266 455 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 4.16 % Allowed : 24.38 % Favored : 71.47 % 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: 1.46 (0.42), residues: 429 helix: 1.73 (0.30), residues: 317 sheet: 2.30 (1.47), residues: 16 loop : -1.94 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.014 0.001 PHE A 341 TYR 0.017 0.002 TYR A 373 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.652 Fit side-chains REVERT: A 200 TYR cc_start: 0.8192 (m-10) cc_final: 0.7792 (m-10) REVERT: A 311 LYS cc_start: 0.7317 (OUTLIER) cc_final: 0.6896 (ttmt) REVERT: A 315 ARG cc_start: 0.6897 (mtt-85) cc_final: 0.6470 (mmm-85) REVERT: A 428 LEU cc_start: 0.6873 (OUTLIER) cc_final: 0.6506 (mp) outliers start: 15 outliers final: 7 residues processed: 56 average time/residue: 1.1852 time to fit residues: 69.0968 Evaluate side-chains 54 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 45 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 9 optimal weight: 0.5980 chunk 38 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 33 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.177661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.127984 restraints weight = 3847.432| |-----------------------------------------------------------------------------| r_work (start): 0.3370 rms_B_bonded: 1.75 r_work: 0.3232 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3119 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3119 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1830 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3341 Z= 0.151 Angle : 0.465 5.151 4536 Z= 0.245 Chirality : 0.039 0.177 575 Planarity : 0.004 0.051 555 Dihedral : 3.444 14.393 455 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 4.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 3.05 % Allowed : 25.76 % Favored : 71.19 % 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: 1.76 (0.42), residues: 429 helix: 1.95 (0.31), residues: 317 sheet: 2.46 (1.41), residues: 16 loop : -1.86 (0.55), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.013 0.001 PHE A 341 TYR 0.018 0.001 TYR A 373 ARG 0.003 0.000 ARG A 447 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.352 Fit side-chains REVERT: A 200 TYR cc_start: 0.8108 (m-10) cc_final: 0.7703 (m-10) REVERT: A 311 LYS cc_start: 0.7233 (OUTLIER) cc_final: 0.6792 (ttmt) REVERT: A 428 LEU cc_start: 0.6854 (OUTLIER) cc_final: 0.6485 (mp) outliers start: 11 outliers final: 8 residues processed: 53 average time/residue: 0.9152 time to fit residues: 50.4177 Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 205 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 411 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 14 optimal weight: 0.6980 chunk 10 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 18 optimal weight: 0.6980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.176722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3464 r_free = 0.3464 target = 0.129765 restraints weight = 3808.746| |-----------------------------------------------------------------------------| r_work (start): 0.3378 rms_B_bonded: 1.93 r_work: 0.3189 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.3073 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3073 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3341 Z= 0.171 Angle : 0.482 5.459 4536 Z= 0.252 Chirality : 0.039 0.173 575 Planarity : 0.004 0.051 555 Dihedral : 3.430 14.322 455 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 4.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 3.05 % Allowed : 25.76 % Favored : 71.19 % 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: 1.72 (0.42), residues: 429 helix: 1.93 (0.30), residues: 317 sheet: 2.43 (1.42), residues: 16 loop : -1.88 (0.54), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.001 HIS A 296 PHE 0.011 0.001 PHE A 341 TYR 0.017 0.001 TYR A 373 ARG 0.003 0.000 ARG A 447 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 858 Ramachandran restraints generated. 429 Oldfield, 0 Emsley, 429 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 47 time to evaluate : 0.341 Fit side-chains REVERT: A 200 TYR cc_start: 0.8114 (m-10) cc_final: 0.7696 (m-10) REVERT: A 311 LYS cc_start: 0.7191 (OUTLIER) cc_final: 0.6834 (ttmt) REVERT: A 315 ARG cc_start: 0.6713 (mtt-85) cc_final: 0.6085 (mmm-85) REVERT: A 428 LEU cc_start: 0.6839 (OUTLIER) cc_final: 0.6451 (mp) outliers start: 11 outliers final: 6 residues processed: 53 average time/residue: 1.0425 time to fit residues: 57.1697 Evaluate side-chains 55 residues out of total 361 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 47 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 149 MET Chi-restraints excluded: chain A residue 225 VAL Chi-restraints excluded: chain A residue 252 GLN Chi-restraints excluded: chain A residue 311 LYS Chi-restraints excluded: chain A residue 339 VAL Chi-restraints excluded: chain A residue 428 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 0 optimal weight: 10.0000 chunk 13 optimal weight: 0.0770 chunk 15 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 1 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 37 optimal weight: 2.9990 overall best weight: 0.7742 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 18 ASN A 41 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3996 r_free = 0.3996 target = 0.176303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.125700 restraints weight = 3832.235| |-----------------------------------------------------------------------------| r_work (start): 0.3355 rms_B_bonded: 1.83 r_work: 0.3211 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3096 rms_B_bonded: 4.37 restraints_weight: 0.2500 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.1856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3341 Z= 0.170 Angle : 0.501 8.488 4536 Z= 0.260 Chirality : 0.043 0.444 575 Planarity : 0.004 0.051 555 Dihedral : 3.438 14.429 455 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Rotamer: Outliers : 2.22 % Allowed : 26.32 % Favored : 71.47 % 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: 1.73 (0.42), residues: 429 helix: 1.99 (0.31), residues: 314 sheet: 2.47 (1.42), residues: 16 loop : -1.98 (0.53), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 19 HIS 0.001 0.001 HIS A 41 PHE 0.014 0.001 PHE A 341 TYR 0.017 0.001 TYR A 373 ARG 0.003 0.000 ARG A 447 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2864.90 seconds wall clock time: 49 minutes 46.76 seconds (2986.76 seconds total)