Starting phenix.real_space_refine on Thu Mar 6 09:15:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u0j_41781/03_2025/8u0j_41781.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u0j_41781/03_2025/8u0j_41781.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u0j_41781/03_2025/8u0j_41781.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u0j_41781/03_2025/8u0j_41781.map" model { file = "/net/cci-nas-00/data/ceres_data/8u0j_41781/03_2025/8u0j_41781.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u0j_41781/03_2025/8u0j_41781.cif" } resolution = 3.1 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= 0.061 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: 6 Type Number sf(0) Gaussians P 48 5.49 5 Mg 1 5.21 5 S 10 5.16 5 C 3466 2.51 5 N 963 2.21 5 O 1169 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 58 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 5657 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 4669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4669 Classifications: {'peptide': 569} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 28, 'TRANS': 540} Chain breaks: 1 Chain: "B" Number of atoms: 290 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 290 Classifications: {'DNA': 14} Modifications used: {'p5*END': 1} Link IDs: {'rna3p': 13} Chain: "D" Number of atoms: 471 Number of conformers: 1 Conformer: "" Number of residues, atoms: 23, 471 Classifications: {'DNA': 23} Link IDs: {'rna3p': 22} Chain: "F" Number of atoms: 226 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 226 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' MG': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.31, per 1000 atoms: 0.76 Number of scatterers: 5657 At special positions: 0 Unit cell: (83.32, 81.6536, 102.484, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 10 16.00 P 48 15.00 Mg 1 11.99 O 1169 8.00 N 963 7.00 C 3466 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: 1.51 Conformation dependent library (CDL) restraints added in 716.1 milliseconds 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1074 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 6 sheets defined 36.7% alpha, 13.2% beta 9 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 1.98 Creating SS restraints... Processing helix chain 'A' and resid 184 through 186 No H-bonds generated for 'chain 'A' and resid 184 through 186' Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 249 through 266 Processing helix chain 'A' and resid 285 through 301 Processing helix chain 'A' and resid 317 through 328 removed outlier: 3.618A pdb=" N THR A 321 " --> pdb=" O ASP A 317 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N HIS A 328 " --> pdb=" O HIS A 324 " (cutoff:3.500A) Processing helix chain 'A' and resid 351 through 355 removed outlier: 3.701A pdb=" N TYR A 355 " --> pdb=" O LYS A 352 " (cutoff:3.500A) Processing helix chain 'A' and resid 361 through 370 removed outlier: 3.834A pdb=" N VAL A 365 " --> pdb=" O ASP A 361 " (cutoff:3.500A) removed outlier: 5.837A pdb=" N ARG A 367 " --> pdb=" O TYR A 363 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N TYR A 370 " --> pdb=" O TYR A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.529A pdb=" N TRP A 384 " --> pdb=" O GLU A 381 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 410 removed outlier: 4.174A pdb=" N VAL A 395 " --> pdb=" O ASN A 391 " (cutoff:3.500A) removed outlier: 3.781A pdb=" N GLU A 396 " --> pdb=" O ARG A 392 " (cutoff:3.500A) Processing helix chain 'A' and resid 436 through 441 removed outlier: 4.015A pdb=" N ARG A 440 " --> pdb=" O SER A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 462 through 473 removed outlier: 3.729A pdb=" N LEU A 471 " --> pdb=" O GLU A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 474 through 480 removed outlier: 4.310A pdb=" N ARG A 478 " --> pdb=" O ASN A 475 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N HIS A 479 " --> pdb=" O ASP A 476 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 528 removed outlier: 3.772A pdb=" N GLU A 521 " --> pdb=" O GLU A 517 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN A 528 " --> pdb=" O GLU A 524 " (cutoff:3.500A) Processing helix chain 'A' and resid 531 through 542 Processing helix chain 'A' and resid 547 through 558 Processing helix chain 'A' and resid 565 through 572 removed outlier: 3.535A pdb=" N GLU A 568 " --> pdb=" O PRO A 565 " (cutoff:3.500A) removed outlier: 4.184A pdb=" N THR A 571 " --> pdb=" O GLU A 568 " (cutoff:3.500A) Processing helix chain 'A' and resid 576 through 589 Processing helix chain 'A' and resid 649 through 657 removed outlier: 3.909A pdb=" N LEU A 655 " --> pdb=" O VAL A 652 " (cutoff:3.500A) removed outlier: 3.892A pdb=" N PHE A 656 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 3.527A pdb=" N ASP A 657 " --> pdb=" O ASN A 654 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 681 removed outlier: 3.808A pdb=" N LYS A 674 " --> pdb=" O PRO A 670 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N HIS A 675 " --> pdb=" O TYR A 671 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 684 No H-bonds generated for 'chain 'A' and resid 682 through 684' Processing sheet with id=AA1, first strand: chain 'A' and resid 136 through 144 removed outlier: 5.757A pdb=" N TYR A 137 " --> pdb=" O ILE A 159 " (cutoff:3.500A) removed outlier: 6.982A pdb=" N ILE A 159 " --> pdb=" O TYR A 137 " (cutoff:3.500A) removed outlier: 5.418A pdb=" N LEU A 139 " --> pdb=" O VAL A 157 " (cutoff:3.500A) removed outlier: 6.411A pdb=" N VAL A 157 " --> pdb=" O LEU A 139 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 181 through 182 Processing sheet with id=AA3, first strand: chain 'A' and resid 236 through 237 Processing sheet with id=AA4, first strand: chain 'A' and resid 334 through 336 removed outlier: 7.052A pdb=" N LEU A 305 " --> pdb=" O GLU A 334 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N ALA A 336 " --> pdb=" O LEU A 305 " (cutoff:3.500A) removed outlier: 6.241A pdb=" N ILE A 307 " --> pdb=" O ALA A 336 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N ASN A 345 " --> pdb=" O GLN A 376 " (cutoff:3.500A) removed outlier: 7.575A pdb=" N CYS A 378 " --> pdb=" O ASN A 345 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N LEU A 347 " --> pdb=" O CYS A 378 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 455 through 460 removed outlier: 7.228A pdb=" N LEU A 638 " --> pdb=" O THR A 504 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N ILE A 506 " --> pdb=" O SER A 636 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N SER A 636 " --> pdb=" O ILE A 506 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 612 through 613 removed outlier: 3.917A pdb=" N PHE A 621 " --> pdb=" O PHE A 612 " (cutoff:3.500A) 154 hydrogen bonds defined for protein. 411 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 20 hydrogen bonds 40 hydrogen bond angles 0 basepair planarities 9 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 1.96 Time building geometry restraints manager: 1.76 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: 940 1.32 - 1.44: 1776 1.44 - 1.57: 3064 1.57 - 1.69: 93 1.69 - 1.81: 16 Bond restraints: 5889 Sorted by residual: bond pdb=" CB VAL A 680 " pdb=" CG1 VAL A 680 " ideal model delta sigma weight residual 1.521 1.418 0.103 3.30e-02 9.18e+02 9.67e+00 bond pdb=" C GLU A 416 " pdb=" N TYR A 417 " ideal model delta sigma weight residual 1.329 1.293 0.036 1.86e-02 2.89e+03 3.78e+00 bond pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta sigma weight residual 1.457 1.480 -0.023 1.29e-02 6.01e+03 3.19e+00 bond pdb=" CG PHE A 656 " pdb=" CD1 PHE A 656 " ideal model delta sigma weight residual 1.384 1.348 0.036 2.10e-02 2.27e+03 2.96e+00 bond pdb=" CB VAL A 251 " pdb=" CG1 VAL A 251 " ideal model delta sigma weight residual 1.521 1.466 0.055 3.30e-02 9.18e+02 2.77e+00 ... (remaining 5884 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 7783 2.00 - 3.99: 329 3.99 - 5.99: 43 5.99 - 7.98: 12 7.98 - 9.98: 2 Bond angle restraints: 8169 Sorted by residual: angle pdb=" C TYR A 363 " pdb=" N GLN A 364 " pdb=" CA GLN A 364 " ideal model delta sigma weight residual 121.54 131.52 -9.98 1.91e+00 2.74e-01 2.73e+01 angle pdb=" C PRO A 563 " pdb=" N LEU A 564 " pdb=" CA LEU A 564 " ideal model delta sigma weight residual 121.61 127.34 -5.73 1.39e+00 5.18e-01 1.70e+01 angle pdb=" C CYS A 378 " pdb=" N TYR A 379 " pdb=" CA TYR A 379 " ideal model delta sigma weight residual 121.48 129.48 -8.00 2.04e+00 2.40e-01 1.54e+01 angle pdb=" N SER A 608 " pdb=" CA SER A 608 " pdb=" C SER A 608 " ideal model delta sigma weight residual 114.09 108.35 5.74 1.55e+00 4.16e-01 1.37e+01 angle pdb=" C GLN A 430 " pdb=" N ARG A 431 " pdb=" CA ARG A 431 " ideal model delta sigma weight residual 120.94 127.94 -7.00 1.90e+00 2.77e-01 1.36e+01 ... (remaining 8164 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 2770 17.94 - 35.88: 404 35.88 - 53.82: 189 53.82 - 71.76: 47 71.76 - 89.70: 9 Dihedral angle restraints: 3419 sinusoidal: 1749 harmonic: 1670 Sorted by residual: dihedral pdb=" CA SER A 437 " pdb=" C SER A 437 " pdb=" N GLU A 438 " pdb=" CA GLU A 438 " ideal model delta harmonic sigma weight residual -180.00 -125.52 -54.48 0 5.00e+00 4.00e-02 1.19e+02 dihedral pdb=" CA GLU A 435 " pdb=" C GLU A 435 " pdb=" N SER A 436 " pdb=" CA SER A 436 " ideal model delta harmonic sigma weight residual -180.00 -140.41 -39.59 0 5.00e+00 4.00e-02 6.27e+01 dihedral pdb=" CA TYR A 220 " pdb=" C TYR A 220 " pdb=" N ILE A 221 " pdb=" CA ILE A 221 " ideal model delta harmonic sigma weight residual 180.00 -158.53 -21.47 0 5.00e+00 4.00e-02 1.84e+01 ... (remaining 3416 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 648 0.051 - 0.102: 186 0.102 - 0.153: 35 0.153 - 0.204: 8 0.204 - 0.255: 1 Chirality restraints: 878 Sorted by residual: chirality pdb=" CA PHE A 656 " pdb=" N PHE A 656 " pdb=" C PHE A 656 " pdb=" CB PHE A 656 " both_signs ideal model delta sigma weight residual False 2.51 2.26 0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CA GLN A 364 " pdb=" N GLN A 364 " pdb=" C GLN A 364 " pdb=" CB GLN A 364 " both_signs ideal model delta sigma weight residual False 2.51 2.31 0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CB VAL A 480 " pdb=" CA VAL A 480 " pdb=" CG1 VAL A 480 " pdb=" CG2 VAL A 480 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.04e-01 ... (remaining 875 not shown) Planarity restraints: 889 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLN A 364 " -0.017 2.00e-02 2.50e+03 3.36e-02 1.13e+01 pdb=" C GLN A 364 " 0.058 2.00e-02 2.50e+03 pdb=" O GLN A 364 " -0.021 2.00e-02 2.50e+03 pdb=" N VAL A 365 " -0.020 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 428 " -0.037 5.00e-02 4.00e+02 5.65e-02 5.12e+00 pdb=" N PRO A 429 " 0.098 5.00e-02 4.00e+02 pdb=" CA PRO A 429 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 429 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 363 " 0.015 2.00e-02 2.50e+03 1.39e-02 3.84e+00 pdb=" CG TYR A 363 " -0.034 2.00e-02 2.50e+03 pdb=" CD1 TYR A 363 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 363 " 0.002 2.00e-02 2.50e+03 pdb=" CE1 TYR A 363 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 363 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 363 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 363 " -0.000 2.00e-02 2.50e+03 ... (remaining 886 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 313 2.72 - 3.26: 5253 3.26 - 3.81: 9454 3.81 - 4.35: 11941 4.35 - 4.90: 19173 Nonbonded interactions: 46134 Sorted by model distance: nonbonded pdb=" OP1 DT B 3 " pdb="MG MG B 101 " model vdw 2.170 2.170 nonbonded pdb=" OH TYR A 620 " pdb=" O VAL A 668 " model vdw 2.204 3.040 nonbonded pdb=" OG SER A 576 " pdb=" OP1 DA D 23 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG A 202 " pdb=" O GLY A 218 " model vdw 2.256 3.120 nonbonded pdb=" O2 DT D 20 " pdb=" N2 DG F 9 " model vdw 2.300 3.120 ... (remaining 46129 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== 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: 2.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.210 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 19.430 Find NCS groups from input model: 0.060 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7035 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 : 0.008 0.103 5889 Z= 0.472 Angle : 0.915 9.980 8169 Z= 0.526 Chirality : 0.050 0.255 878 Planarity : 0.006 0.057 889 Dihedral : 20.282 89.698 2345 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.96 % Favored : 92.04 % Rotamer: Outliers : 0.00 % Allowed : 0.39 % Favored : 99.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.07 (0.34), residues: 565 helix: 0.11 (0.40), residues: 154 sheet: -0.19 (0.53), residues: 90 loop : -1.30 (0.34), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 444 HIS 0.006 0.002 HIS A 660 PHE 0.025 0.003 PHE A 685 TYR 0.034 0.003 TYR A 363 ARG 0.017 0.001 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.549 Fit side-chains REVERT: A 302 GLU cc_start: 0.7306 (tp30) cc_final: 0.6769 (tm-30) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.2169 time to fit residues: 23.2439 Evaluate side-chains 72 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 35 optimal weight: 0.9980 chunk 54 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4539 r_free = 0.4539 target = 0.229186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.182102 restraints weight = 6447.712| |-----------------------------------------------------------------------------| r_work (start): 0.4098 rms_B_bonded: 3.22 r_work: 0.3944 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3944 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7145 moved from start: 0.1215 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 5889 Z= 0.280 Angle : 0.657 7.602 8169 Z= 0.361 Chirality : 0.043 0.155 878 Planarity : 0.006 0.044 889 Dihedral : 23.077 76.041 1166 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.37 % Favored : 93.63 % Rotamer: Outliers : 0.98 % Allowed : 8.24 % Favored : 90.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.79 (0.35), residues: 565 helix: 0.70 (0.41), residues: 157 sheet: -0.25 (0.51), residues: 95 loop : -1.28 (0.35), residues: 313 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 585 HIS 0.004 0.001 HIS A 281 PHE 0.025 0.002 PHE A 611 TYR 0.016 0.002 TYR A 671 ARG 0.003 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 83 time to evaluate : 0.584 Fit side-chains REVERT: A 302 GLU cc_start: 0.7854 (tp30) cc_final: 0.7177 (tm-30) REVERT: A 440 ARG cc_start: 0.6780 (mmm160) cc_final: 0.5812 (mmm160) outliers start: 5 outliers final: 3 residues processed: 85 average time/residue: 0.1968 time to fit residues: 21.6580 Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 77 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 597 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 43 optimal weight: 0.9990 chunk 50 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 17 optimal weight: 0.9990 chunk 52 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 38 optimal weight: 0.3980 chunk 11 optimal weight: 0.8980 chunk 51 optimal weight: 0.5980 chunk 47 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4517 r_free = 0.4517 target = 0.227505 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4113 r_free = 0.4113 target = 0.183121 restraints weight = 6368.901| |-----------------------------------------------------------------------------| r_work (start): 0.4120 rms_B_bonded: 3.06 r_work: 0.3964 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1662 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5889 Z= 0.256 Angle : 0.614 6.968 8169 Z= 0.337 Chirality : 0.041 0.153 878 Planarity : 0.005 0.044 889 Dihedral : 22.974 74.250 1166 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.08 % Favored : 92.92 % Rotamer: Outliers : 1.57 % Allowed : 11.96 % Favored : 86.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.48 (0.36), residues: 565 helix: 1.11 (0.41), residues: 156 sheet: 0.02 (0.52), residues: 94 loop : -1.20 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 585 HIS 0.005 0.001 HIS A 281 PHE 0.017 0.002 PHE A 685 TYR 0.014 0.002 TYR A 671 ARG 0.003 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 83 time to evaluate : 0.567 Fit side-chains REVERT: A 302 GLU cc_start: 0.7853 (tp30) cc_final: 0.7253 (tm-30) REVERT: A 440 ARG cc_start: 0.6722 (mmm160) cc_final: 0.6001 (mmm160) outliers start: 8 outliers final: 5 residues processed: 86 average time/residue: 0.2016 time to fit residues: 22.2865 Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 75 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 632 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 0.0470 chunk 11 optimal weight: 0.7980 chunk 58 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 1 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 32 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 overall best weight: 0.8880 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 537 GLN A 654 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4528 r_free = 0.4528 target = 0.227803 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4089 r_free = 0.4089 target = 0.180321 restraints weight = 6618.533| |-----------------------------------------------------------------------------| r_work (start): 0.4090 rms_B_bonded: 3.27 r_work: 0.3930 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3930 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7170 moved from start: 0.1882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5889 Z= 0.301 Angle : 0.631 6.408 8169 Z= 0.344 Chirality : 0.042 0.156 878 Planarity : 0.005 0.042 889 Dihedral : 23.027 75.090 1166 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 2.35 % Allowed : 13.33 % Favored : 84.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.48 (0.36), residues: 565 helix: 1.12 (0.41), residues: 156 sheet: -0.03 (0.52), residues: 94 loop : -1.18 (0.36), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 444 HIS 0.004 0.001 HIS A 281 PHE 0.028 0.002 PHE A 611 TYR 0.014 0.002 TYR A 671 ARG 0.003 0.000 ARG A 686 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 80 time to evaluate : 0.558 Fit side-chains REVERT: A 302 GLU cc_start: 0.7875 (tp30) cc_final: 0.7287 (tm-30) REVERT: A 440 ARG cc_start: 0.6700 (mmm160) cc_final: 0.5834 (mmm160) REVERT: A 611 PHE cc_start: 0.7444 (t80) cc_final: 0.7082 (t80) outliers start: 12 outliers final: 8 residues processed: 87 average time/residue: 0.2103 time to fit residues: 23.4640 Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 53 optimal weight: 0.9990 chunk 9 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 482 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.227419 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.180191 restraints weight = 6477.440| |-----------------------------------------------------------------------------| r_work (start): 0.4079 rms_B_bonded: 3.21 r_work: 0.3922 rms_B_bonded: 4.13 restraints_weight: 0.5000 r_work (final): 0.3922 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7172 moved from start: 0.2098 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 5889 Z= 0.298 Angle : 0.626 6.194 8169 Z= 0.341 Chirality : 0.041 0.155 878 Planarity : 0.005 0.044 889 Dihedral : 22.997 74.294 1166 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.43 % Favored : 92.57 % Rotamer: Outliers : 2.16 % Allowed : 13.92 % Favored : 83.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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 (0.36), residues: 565 helix: 1.14 (0.41), residues: 157 sheet: -0.18 (0.51), residues: 92 loop : -1.17 (0.36), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 444 HIS 0.003 0.001 HIS A 281 PHE 0.024 0.002 PHE A 611 TYR 0.013 0.002 TYR A 671 ARG 0.002 0.000 ARG A 686 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 78 time to evaluate : 0.563 Fit side-chains REVERT: A 302 GLU cc_start: 0.7819 (tp30) cc_final: 0.7293 (tm-30) REVERT: A 341 ARG cc_start: 0.7196 (OUTLIER) cc_final: 0.6683 (mtp180) REVERT: A 440 ARG cc_start: 0.6570 (mmm160) cc_final: 0.5570 (mmm160) REVERT: A 578 ASP cc_start: 0.8338 (t0) cc_final: 0.8132 (t0) outliers start: 11 outliers final: 8 residues processed: 83 average time/residue: 0.1992 time to fit residues: 21.2341 Evaluate side-chains 79 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 70 time to evaluate : 0.499 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 632 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.0870 chunk 30 optimal weight: 0.0980 chunk 3 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 47 optimal weight: 0.1980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 overall best weight: 0.3758 ------------------------------------------------------------------------------- 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 = 0.4580 r_free = 0.4580 target = 0.233626 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.187243 restraints weight = 6493.332| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.24 r_work: 0.3990 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.3990 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2411 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 5889 Z= 0.193 Angle : 0.572 6.147 8169 Z= 0.314 Chirality : 0.039 0.148 878 Planarity : 0.005 0.046 889 Dihedral : 22.789 67.985 1166 Min Nonbonded Distance : 2.286 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.66 % Favored : 94.34 % Rotamer: Outliers : 1.76 % Allowed : 16.47 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.37 % 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: -0.18 (0.36), residues: 565 helix: 1.53 (0.42), residues: 157 sheet: -0.12 (0.52), residues: 92 loop : -0.99 (0.37), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 444 HIS 0.002 0.001 HIS A 643 PHE 0.012 0.002 PHE A 685 TYR 0.012 0.001 TYR A 491 ARG 0.002 0.000 ARG A 686 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 0.540 Fit side-chains REVERT: A 302 GLU cc_start: 0.7818 (tp30) cc_final: 0.7253 (tm-30) REVERT: A 341 ARG cc_start: 0.7162 (OUTLIER) cc_final: 0.6703 (mtp85) REVERT: A 417 TYR cc_start: 0.7740 (m-80) cc_final: 0.7402 (m-80) REVERT: A 440 ARG cc_start: 0.6486 (mmm160) cc_final: 0.5455 (mmm160) REVERT: A 578 ASP cc_start: 0.8302 (t0) cc_final: 0.8095 (t0) REVERT: A 619 MET cc_start: 0.5685 (mtm) cc_final: 0.5390 (mtm) outliers start: 9 outliers final: 6 residues processed: 82 average time/residue: 0.1935 time to fit residues: 20.5279 Evaluate side-chains 78 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.573 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 328 HIS Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 23 optimal weight: 0.7980 chunk 43 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 54 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.4545 r_free = 0.4545 target = 0.229577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4111 r_free = 0.4111 target = 0.182697 restraints weight = 6529.918| |-----------------------------------------------------------------------------| r_work (start): 0.4105 rms_B_bonded: 3.22 r_work: 0.3947 rms_B_bonded: 4.15 restraints_weight: 0.5000 r_work (final): 0.3947 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7146 moved from start: 0.2395 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 5889 Z= 0.272 Angle : 0.605 5.927 8169 Z= 0.330 Chirality : 0.041 0.154 878 Planarity : 0.005 0.046 889 Dihedral : 22.985 75.351 1166 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 1.96 % Allowed : 16.67 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.27 (0.36), residues: 565 helix: 1.51 (0.41), residues: 156 sheet: -0.19 (0.52), residues: 92 loop : -1.07 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 444 HIS 0.002 0.001 HIS A 643 PHE 0.016 0.002 PHE A 685 TYR 0.013 0.002 TYR A 671 ARG 0.002 0.000 ARG A 367 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.549 Fit side-chains REVERT: A 302 GLU cc_start: 0.7862 (tp30) cc_final: 0.7199 (tm-30) REVERT: A 417 TYR cc_start: 0.7798 (m-80) cc_final: 0.7419 (m-80) REVERT: A 440 ARG cc_start: 0.6560 (mmm160) cc_final: 0.5391 (mmm160) REVERT: A 619 MET cc_start: 0.5739 (mtm) cc_final: 0.5427 (mtm) outliers start: 10 outliers final: 10 residues processed: 77 average time/residue: 0.2117 time to fit residues: 21.0002 Evaluate side-chains 76 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.540 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 489 VAL Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 53 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 0.2980 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 0.1980 chunk 57 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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 = 0.4562 r_free = 0.4562 target = 0.231499 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.184934 restraints weight = 6380.863| |-----------------------------------------------------------------------------| r_work (start): 0.4126 rms_B_bonded: 3.19 r_work: 0.3972 rms_B_bonded: 4.11 restraints_weight: 0.5000 r_work (final): 0.3972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7111 moved from start: 0.2529 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 5889 Z= 0.235 Angle : 0.594 6.418 8169 Z= 0.324 Chirality : 0.040 0.151 878 Planarity : 0.005 0.044 889 Dihedral : 22.903 71.360 1166 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 10.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.55 % Favored : 93.45 % Rotamer: Outliers : 1.76 % Allowed : 17.25 % Favored : 80.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.18 (0.36), residues: 565 helix: 1.61 (0.42), residues: 156 sheet: -0.08 (0.52), residues: 92 loop : -1.05 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 444 HIS 0.002 0.001 HIS A 643 PHE 0.028 0.002 PHE A 621 TYR 0.012 0.001 TYR A 671 ARG 0.001 0.000 ARG A 615 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 72 time to evaluate : 0.538 Fit side-chains REVERT: A 302 GLU cc_start: 0.7813 (tp30) cc_final: 0.7146 (tm-30) REVERT: A 341 ARG cc_start: 0.7133 (OUTLIER) cc_final: 0.6651 (mtp180) REVERT: A 417 TYR cc_start: 0.7717 (m-80) cc_final: 0.7330 (m-80) REVERT: A 440 ARG cc_start: 0.6457 (mmm160) cc_final: 0.5214 (mmm160) REVERT: A 611 PHE cc_start: 0.7128 (t80) cc_final: 0.6918 (t80) REVERT: A 619 MET cc_start: 0.5779 (mtm) cc_final: 0.5460 (mtm) outliers start: 9 outliers final: 8 residues processed: 75 average time/residue: 0.1951 time to fit residues: 18.9260 Evaluate side-chains 77 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.508 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 241 GLU Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 316 THR Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 468 ASP Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 597 ILE Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 6 optimal weight: 0.1980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.1980 chunk 12 optimal weight: 0.2980 chunk 23 optimal weight: 0.7980 chunk 26 optimal weight: 0.8980 chunk 27 optimal weight: 1.9990 chunk 49 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 31 optimal weight: 0.5980 chunk 4 optimal weight: 3.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- 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 = 0.4582 r_free = 0.4582 target = 0.233852 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4159 r_free = 0.4159 target = 0.187362 restraints weight = 6430.194| |-----------------------------------------------------------------------------| r_work (start): 0.4151 rms_B_bonded: 3.21 r_work: 0.3996 rms_B_bonded: 4.14 restraints_weight: 0.5000 r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7075 moved from start: 0.2671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5889 Z= 0.195 Angle : 0.567 6.281 8169 Z= 0.310 Chirality : 0.039 0.150 878 Planarity : 0.005 0.046 889 Dihedral : 22.830 70.468 1166 Min Nonbonded Distance : 2.349 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 1.18 % Allowed : 17.45 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: -0.01 (0.36), residues: 565 helix: 1.78 (0.42), residues: 156 sheet: 0.07 (0.52), residues: 92 loop : -0.98 (0.37), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 444 HIS 0.002 0.001 HIS A 292 PHE 0.022 0.002 PHE A 621 TYR 0.011 0.001 TYR A 671 ARG 0.001 0.000 ARG A 598 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 74 time to evaluate : 0.875 Fit side-chains REVERT: A 302 GLU cc_start: 0.7830 (tp30) cc_final: 0.7154 (tm-30) REVERT: A 341 ARG cc_start: 0.7140 (OUTLIER) cc_final: 0.6687 (mtp180) REVERT: A 417 TYR cc_start: 0.7671 (m-80) cc_final: 0.7280 (m-80) REVERT: A 435 GLU cc_start: 0.7450 (mm-30) cc_final: 0.6745 (pm20) REVERT: A 440 ARG cc_start: 0.6395 (mmm160) cc_final: 0.5161 (mmm160) REVERT: A 611 PHE cc_start: 0.7038 (t80) cc_final: 0.6773 (t80) REVERT: A 619 MET cc_start: 0.5626 (mtm) cc_final: 0.5347 (mtm) outliers start: 6 outliers final: 5 residues processed: 77 average time/residue: 0.2071 time to fit residues: 20.8290 Evaluate side-chains 77 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 0.600 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 288 ILE Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 26 optimal weight: 0.3980 chunk 14 optimal weight: 0.0980 chunk 25 optimal weight: 0.0980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 19 optimal weight: 0.2980 chunk 4 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 overall best weight: 0.2780 ------------------------------------------------------------------------------- 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 = 0.4606 r_free = 0.4606 target = 0.236588 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4190 r_free = 0.4190 target = 0.190396 restraints weight = 6566.226| |-----------------------------------------------------------------------------| r_work (start): 0.4182 rms_B_bonded: 3.26 r_work: 0.4024 rms_B_bonded: 4.22 restraints_weight: 0.5000 r_work (final): 0.4024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7026 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5889 Z= 0.177 Angle : 0.555 6.041 8169 Z= 0.304 Chirality : 0.038 0.146 878 Planarity : 0.005 0.045 889 Dihedral : 22.789 69.743 1166 Min Nonbonded Distance : 2.400 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.19 % Favored : 93.81 % Rotamer: Outliers : 0.98 % Allowed : 17.84 % Favored : 81.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.15 (0.36), residues: 565 helix: 1.96 (0.42), residues: 157 sheet: 0.09 (0.51), residues: 93 loop : -0.89 (0.37), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 492 HIS 0.002 0.001 HIS A 292 PHE 0.022 0.001 PHE A 621 TYR 0.011 0.001 TYR A 491 ARG 0.001 0.000 ARG A 198 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1130 Ramachandran restraints generated. 565 Oldfield, 0 Emsley, 565 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 76 time to evaluate : 0.542 Fit side-chains REVERT: A 302 GLU cc_start: 0.7779 (tp30) cc_final: 0.7286 (tm-30) REVERT: A 341 ARG cc_start: 0.7130 (OUTLIER) cc_final: 0.6687 (mtp85) REVERT: A 435 GLU cc_start: 0.7488 (mm-30) cc_final: 0.7142 (pm20) REVERT: A 440 ARG cc_start: 0.6325 (mmm160) cc_final: 0.5107 (mmm160) REVERT: A 611 PHE cc_start: 0.6935 (t80) cc_final: 0.6657 (t80) REVERT: A 619 MET cc_start: 0.5581 (mtm) cc_final: 0.5321 (mtm) outliers start: 5 outliers final: 4 residues processed: 78 average time/residue: 0.1960 time to fit residues: 19.9079 Evaluate side-chains 82 residues out of total 510 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 77 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 261 LEU Chi-restraints excluded: chain A residue 341 ARG Chi-restraints excluded: chain A residue 490 ILE Chi-restraints excluded: chain A residue 504 THR Chi-restraints excluded: chain A residue 656 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 14 optimal weight: 0.0270 chunk 28 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 overall best weight: 0.3638 ------------------------------------------------------------------------------- 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 = 0.4602 r_free = 0.4602 target = 0.236042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.189563 restraints weight = 6495.346| |-----------------------------------------------------------------------------| r_work (start): 0.4174 rms_B_bonded: 3.23 r_work: 0.4016 rms_B_bonded: 4.20 restraints_weight: 0.5000 r_work (final): 0.4016 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7038 moved from start: 0.2946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5889 Z= 0.189 Angle : 0.563 5.973 8169 Z= 0.306 Chirality : 0.039 0.149 878 Planarity : 0.005 0.046 889 Dihedral : 22.822 71.674 1166 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.02 % Favored : 93.98 % Rotamer: Outliers : 1.37 % Allowed : 17.84 % Favored : 80.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.19 % 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: 0.03 (0.37), residues: 565 helix: 2.03 (0.42), residues: 156 sheet: -0.68 (0.49), residues: 110 loop : -0.79 (0.38), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 444 HIS 0.004 0.001 HIS A 409 PHE 0.018 0.002 PHE A 621 TYR 0.012 0.001 TYR A 671 ARG 0.003 0.000 ARG A 411 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3115.24 seconds wall clock time: 54 minutes 30.59 seconds (3270.59 seconds total)