Starting phenix.real_space_refine on Mon Feb 10 20:24:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/6zs5_11388/02_2025/6zs5_11388.cif Found real_map, /net/cci-nas-00/data/ceres_data/6zs5_11388/02_2025/6zs5_11388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/6zs5_11388/02_2025/6zs5_11388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/6zs5_11388/02_2025/6zs5_11388.map" model { file = "/net/cci-nas-00/data/ceres_data/6zs5_11388/02_2025/6zs5_11388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/6zs5_11388/02_2025/6zs5_11388.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.082 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 1261 2.51 5 N 341 2.21 5 O 413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2036 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 911 Number of conformers: 1 Conformer: "" Number of residues, atoms: 116, 911 Classifications: {'peptide': 116} Link IDs: {'PTRANS': 4, 'TRANS': 111} Chain: "D" Number of atoms: 1036 Number of conformers: 1 Conformer: "" Number of residues, atoms: 141, 1036 Classifications: {'peptide': 141} Incomplete info: {'backbone_only': 12} Link IDs: {'PTRANS': 6, 'TRANS': 134} Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 61 Unresolved non-hydrogen angles: 89 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 15 Planarities with less than four sites: {'PHE:plan': 1, 'GLN:plan1': 3, 'TYR:plan': 2} Unresolved non-hydrogen planarities: 35 Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "C" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 2.64, per 1000 atoms: 1.30 Number of scatterers: 2036 At special positions: 0 Unit cell: (72.628, 71.544, 88.888, 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 413 8.00 N 341 7.00 C 1261 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 335 " - pdb=" SG CYS A 425 " distance=2.03 Simple disulfide: pdb=" SG CYS A 366 " - pdb=" SG CYS A 389 " distance=2.04 Simple disulfide: pdb=" SG CYS D 506 " - pdb=" SG CYS D 566 " distance=2.03 Simple disulfide: pdb=" SG CYS D 527 " - pdb=" SG CYS D 582 " distance=1.59 Simple disulfide: pdb=" SG CYS D 571 " - pdb=" SG CYS D 578 " distance=1.89 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 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " NAG-ASN " NAG B 1 " - " ASN A 396 " " NAG C 1 " - " ASN D 513 " Time building additional restraints: 0.72 Conformation dependent library (CDL) restraints added in 338.1 milliseconds 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 456 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 43.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 331 through 333 removed outlier: 3.661A pdb=" N VAL A 342 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 358 through 360 removed outlier: 3.662A pdb=" N ASN A 404 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 419 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 392 through 395 removed outlier: 3.662A pdb=" N ASN A 404 " --> pdb=" O PHE A 423 " (cutoff:3.500A) removed outlier: 4.178A pdb=" N ILE A 419 " --> pdb=" O LEU A 408 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 430 through 434 removed outlier: 6.680A pdb=" N TYR D 563 " --> pdb=" O ALA D 508 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N ALA D 508 " --> pdb=" O TYR D 563 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N HIS D 565 " --> pdb=" O CYS D 506 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N CYS D 506 " --> pdb=" O HIS D 565 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N GLU D 567 " --> pdb=" O THR D 504 " (cutoff:3.500A) removed outlier: 6.486A pdb=" N CYS D 506 " --> pdb=" O ILE D 522 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 438 through 440 removed outlier: 6.863A pdb=" N ALA A 438 " --> pdb=" O VAL D 477 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'D' and resid 458 through 463 removed outlier: 4.017A pdb=" N TYR D 486 " --> pdb=" O PHE D 463 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N VAL D 550 " --> pdb=" O LEU D 485 " (cutoff:3.500A) removed outlier: 7.112A pdb=" N ARG D 547 " --> pdb=" O VAL D 538 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N VAL D 538 " --> pdb=" O ARG D 547 " (cutoff:3.500A) 61 hydrogen bonds defined for protein. 162 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: 0.49 Time building geometry restraints manager: 0.80 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 332 1.31 - 1.44: 558 1.44 - 1.57: 1145 1.57 - 1.70: 3 1.70 - 1.83: 31 Bond restraints: 2069 Sorted by residual: bond pdb=" CA SER D 583 " pdb=" C SER D 583 " ideal model delta sigma weight residual 1.520 1.462 0.059 1.20e-02 6.94e+03 2.41e+01 bond pdb=" C SER D 583 " pdb=" O SER D 583 " ideal model delta sigma weight residual 1.234 1.180 0.055 1.15e-02 7.56e+03 2.28e+01 bond pdb=" CA THR D 581 " pdb=" C THR D 581 " ideal model delta sigma weight residual 1.523 1.484 0.039 1.21e-02 6.83e+03 1.06e+01 bond pdb=" CA SER D 583 " pdb=" CB SER D 583 " ideal model delta sigma weight residual 1.533 1.479 0.054 1.69e-02 3.50e+03 1.02e+01 bond pdb=" N THR D 581 " pdb=" CA THR D 581 " ideal model delta sigma weight residual 1.460 1.423 0.036 1.20e-02 6.94e+03 9.24e+00 ... (remaining 2064 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.18: 2659 2.18 - 4.37: 101 4.37 - 6.55: 28 6.55 - 8.74: 3 8.74 - 10.92: 1 Bond angle restraints: 2792 Sorted by residual: angle pdb=" C LYS D 579 " pdb=" N PRO D 580 " pdb=" CA PRO D 580 " ideal model delta sigma weight residual 119.76 125.33 -5.57 1.03e+00 9.43e-01 2.92e+01 angle pdb=" N GLY A 387 " pdb=" CA GLY A 387 " pdb=" C GLY A 387 " ideal model delta sigma weight residual 112.34 123.26 -10.92 2.04e+00 2.40e-01 2.87e+01 angle pdb=" N THR D 581 " pdb=" CA THR D 581 " pdb=" C THR D 581 " ideal model delta sigma weight residual 108.02 100.12 7.90 1.75e+00 3.27e-01 2.04e+01 angle pdb=" C THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta sigma weight residual 110.74 104.22 6.52 1.61e+00 3.86e-01 1.64e+01 angle pdb=" CA PRO D 580 " pdb=" C PRO D 580 " pdb=" N THR D 581 " ideal model delta sigma weight residual 115.56 110.66 4.90 1.27e+00 6.20e-01 1.49e+01 ... (remaining 2787 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.21: 1238 24.21 - 48.41: 63 48.41 - 72.62: 6 72.62 - 96.82: 18 96.82 - 121.02: 9 Dihedral angle restraints: 1334 sinusoidal: 613 harmonic: 721 Sorted by residual: dihedral pdb=" CA LYS A 346 " pdb=" C LYS A 346 " pdb=" N CYS A 347 " pdb=" CA CYS A 347 " ideal model delta harmonic sigma weight residual 180.00 150.31 29.69 0 5.00e+00 4.00e-02 3.53e+01 dihedral pdb=" N THR D 581 " pdb=" C THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta harmonic sigma weight residual 123.40 109.35 14.05 0 2.50e+00 1.60e-01 3.16e+01 dihedral pdb=" C THR D 581 " pdb=" N THR D 581 " pdb=" CA THR D 581 " pdb=" CB THR D 581 " ideal model delta harmonic sigma weight residual -122.00 -108.06 -13.94 0 2.50e+00 1.60e-01 3.11e+01 ... (remaining 1331 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 256 0.068 - 0.137: 68 0.137 - 0.205: 4 0.205 - 0.273: 3 0.273 - 0.342: 2 Chirality restraints: 333 Sorted by residual: chirality pdb=" CA THR D 581 " pdb=" N THR D 581 " pdb=" C THR D 581 " pdb=" CB THR D 581 " both_signs ideal model delta sigma weight residual False 2.53 2.87 -0.34 2.00e-01 2.50e+01 2.92e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.62 0.34 2.00e-01 2.50e+01 2.91e+00 chirality pdb=" C2 BMA B 3 " pdb=" C1 BMA B 3 " pdb=" C3 BMA B 3 " pdb=" O2 BMA B 3 " both_signs ideal model delta sigma weight residual False 2.47 2.74 -0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 330 not shown) Planarity restraints: 354 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP D 525 " -0.015 2.00e-02 2.50e+03 3.05e-02 9.30e+00 pdb=" CG ASP D 525 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP D 525 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP D 525 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP A 386 " -0.012 2.00e-02 2.50e+03 2.46e-02 6.04e+00 pdb=" CG ASP A 386 " 0.042 2.00e-02 2.50e+03 pdb=" OD1 ASP A 386 " -0.015 2.00e-02 2.50e+03 pdb=" OD2 ASP A 386 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLY A 387 " -0.041 5.00e-02 4.00e+02 6.06e-02 5.87e+00 pdb=" N PRO A 388 " 0.105 5.00e-02 4.00e+02 pdb=" CA PRO A 388 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 388 " -0.035 5.00e-02 4.00e+02 ... (remaining 351 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 186 2.74 - 3.28: 1655 3.28 - 3.82: 2977 3.82 - 4.36: 3207 4.36 - 4.90: 5904 Nonbonded interactions: 13929 Sorted by model distance: nonbonded pdb=" O THR D 581 " pdb=" OG1 THR D 581 " model vdw 2.202 3.040 nonbonded pdb=" OD1 ASP D 532 " pdb=" OG1 THR D 534 " model vdw 2.319 3.040 nonbonded pdb=" OG SER A 362 " pdb=" OD1 ASN A 404 " model vdw 2.342 3.040 nonbonded pdb=" OG SER D 543 " pdb=" N SER D 544 " model vdw 2.348 3.120 nonbonded pdb=" OH TYR A 402 " pdb=" OD2 ASP D 495 " model vdw 2.369 3.040 ... (remaining 13924 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.480 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.030 Process input model: 11.160 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 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: 0.010 Load rotamer database and sin/cos tables:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 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 0.067 2069 Z= 0.572 Angle : 1.087 10.920 2792 Z= 0.594 Chirality : 0.067 0.342 333 Planarity : 0.008 0.061 352 Dihedral : 21.400 121.023 863 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.00 % Allowed : 7.91 % Favored : 92.09 % Cbeta Deviations : 0.44 % 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: -2.98 (0.45), residues: 253 helix: None (None), residues: 0 sheet: -1.19 (0.53), residues: 92 loop : -2.61 (0.37), residues: 161 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP A 377 HIS 0.002 0.001 HIS D 565 PHE 0.024 0.003 PHE A 423 TYR 0.027 0.003 TYR D 486 ARG 0.003 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.247 Fit side-chains REVERT: A 375 ARG cc_start: 0.7475 (mtp180) cc_final: 0.6656 (tpt170) outliers start: 0 outliers final: 0 residues processed: 64 average time/residue: 0.2463 time to fit residues: 17.1963 Evaluate side-chains 45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3508 r_free = 0.3508 target = 0.085423 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.072410 restraints weight = 6059.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.074261 restraints weight = 3321.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3333 r_free = 0.3333 target = 0.075548 restraints weight = 2203.308| |-----------------------------------------------------------------------------| r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2069 Z= 0.213 Angle : 0.737 7.672 2792 Z= 0.365 Chirality : 0.048 0.173 333 Planarity : 0.005 0.046 352 Dihedral : 18.266 119.742 420 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 6.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 4.19 % Allowed : 23.26 % Favored : 72.56 % 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: -2.26 (0.47), residues: 253 helix: None (None), residues: 0 sheet: -0.51 (0.50), residues: 100 loop : -2.31 (0.42), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 377 HIS 0.001 0.001 HIS A 331 PHE 0.010 0.001 PHE D 548 TYR 0.014 0.001 TYR D 486 ARG 0.005 0.001 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 47 time to evaluate : 0.231 Fit side-chains REVERT: A 375 ARG cc_start: 0.7388 (mtp180) cc_final: 0.6533 (tpt170) outliers start: 9 outliers final: 4 residues processed: 51 average time/residue: 0.1703 time to fit residues: 9.9351 Evaluate side-chains 45 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.216 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 525 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 2 optimal weight: 0.0060 chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 4.9990 chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 0.0050 chunk 1 optimal weight: 0.8980 chunk 0 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 overall best weight: 0.7212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN D 524 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.085927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.072769 restraints weight = 6042.697| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.074703 restraints weight = 3293.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.076050 restraints weight = 2163.103| |-----------------------------------------------------------------------------| r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7844 moved from start: 0.2999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2069 Z= 0.176 Angle : 0.667 6.708 2792 Z= 0.330 Chirality : 0.048 0.212 333 Planarity : 0.004 0.040 352 Dihedral : 14.385 115.339 420 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.19 % Allowed : 23.72 % Favored : 72.09 % 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: -1.78 (0.48), residues: 253 helix: None (None), residues: 0 sheet: -0.06 (0.50), residues: 98 loop : -2.06 (0.44), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 377 HIS 0.001 0.000 HIS D 565 PHE 0.009 0.001 PHE D 548 TYR 0.010 0.001 TYR D 486 ARG 0.003 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 41 time to evaluate : 0.244 Fit side-chains REVERT: A 365 ARG cc_start: 0.8313 (mtm110) cc_final: 0.7860 (mtm110) REVERT: A 375 ARG cc_start: 0.7369 (mtp180) cc_final: 0.6630 (tpt170) REVERT: D 576 GLU cc_start: 0.8132 (mt-10) cc_final: 0.7846 (mp0) outliers start: 9 outliers final: 5 residues processed: 47 average time/residue: 0.1635 time to fit residues: 8.8268 Evaluate side-chains 43 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 348 GLN Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 509 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 0.0970 chunk 2 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 overall best weight: 0.7378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.085774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.072947 restraints weight = 5820.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3319 r_free = 0.3319 target = 0.074829 restraints weight = 3166.199| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3345 r_free = 0.3345 target = 0.076148 restraints weight = 2079.393| |-----------------------------------------------------------------------------| r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7841 moved from start: 0.3213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2069 Z= 0.185 Angle : 0.649 6.442 2792 Z= 0.324 Chirality : 0.048 0.220 333 Planarity : 0.004 0.038 352 Dihedral : 14.055 115.728 420 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.37 % Favored : 97.63 % Rotamer: Outliers : 5.58 % Allowed : 20.47 % Favored : 73.95 % 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 (0.48), residues: 253 helix: None (None), residues: 0 sheet: 0.16 (0.53), residues: 90 loop : -2.04 (0.42), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 377 HIS 0.001 0.000 HIS A 331 PHE 0.009 0.001 PHE A 423 TYR 0.010 0.001 TYR D 486 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 42 time to evaluate : 0.229 Fit side-chains REVERT: A 365 ARG cc_start: 0.8329 (mtm110) cc_final: 0.7892 (mtm110) REVERT: A 375 ARG cc_start: 0.7344 (mtp180) cc_final: 0.6618 (tpt170) REVERT: A 420 LYS cc_start: 0.7903 (OUTLIER) cc_final: 0.7693 (ptmt) REVERT: A 431 MET cc_start: 0.8844 (mmp) cc_final: 0.8587 (mmp) REVERT: D 460 MET cc_start: 0.8199 (mtm) cc_final: 0.7829 (mtm) REVERT: D 567 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7723 (pt0) REVERT: D 576 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8095 (mp0) outliers start: 12 outliers final: 7 residues processed: 48 average time/residue: 0.1764 time to fit residues: 9.6683 Evaluate side-chains 47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 567 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 17 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 348 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3518 r_free = 0.3518 target = 0.085838 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.073020 restraints weight = 6082.032| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.074981 restraints weight = 3217.412| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.076307 restraints weight = 2074.456| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7845 moved from start: 0.3465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2069 Z= 0.194 Angle : 0.637 5.778 2792 Z= 0.314 Chirality : 0.047 0.227 333 Planarity : 0.004 0.040 352 Dihedral : 13.279 114.978 420 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 6.98 % Allowed : 19.07 % Favored : 73.95 % 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: -1.62 (0.49), residues: 253 helix: None (None), residues: 0 sheet: 0.20 (0.53), residues: 90 loop : -1.95 (0.44), residues: 163 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 377 HIS 0.001 0.000 HIS A 331 PHE 0.010 0.001 PHE A 423 TYR 0.012 0.001 TYR D 486 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 41 time to evaluate : 0.249 Fit side-chains REVERT: A 365 ARG cc_start: 0.8349 (mtm110) cc_final: 0.7899 (mtm110) REVERT: A 375 ARG cc_start: 0.7371 (mtp180) cc_final: 0.6664 (tpt170) REVERT: A 431 MET cc_start: 0.8829 (mmp) cc_final: 0.8628 (mmp) REVERT: D 460 MET cc_start: 0.8287 (mtm) cc_final: 0.8073 (mtm) REVERT: D 567 GLU cc_start: 0.7961 (OUTLIER) cc_final: 0.7754 (pt0) REVERT: D 576 GLU cc_start: 0.8586 (mt-10) cc_final: 0.8242 (mp0) outliers start: 15 outliers final: 8 residues processed: 48 average time/residue: 0.1800 time to fit residues: 9.8698 Evaluate side-chains 47 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 38 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 357 VAL Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 567 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.7980 chunk 23 optimal weight: 0.9980 chunk 16 optimal weight: 2.9990 chunk 8 optimal weight: 4.9990 chunk 22 optimal weight: 0.9980 chunk 1 optimal weight: 6.9990 chunk 4 optimal weight: 7.9990 chunk 6 optimal weight: 0.8980 chunk 21 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 565 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.085689 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.072939 restraints weight = 6027.328| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.074884 restraints weight = 3177.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.076201 restraints weight = 2048.262| |-----------------------------------------------------------------------------| r_work (final): 0.3347 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 moved from start: 0.3679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2069 Z= 0.185 Angle : 0.643 5.840 2792 Z= 0.312 Chirality : 0.047 0.229 333 Planarity : 0.003 0.039 352 Dihedral : 12.741 114.428 420 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.65 % Allowed : 22.33 % Favored : 73.02 % 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: -1.54 (0.49), residues: 253 helix: None (None), residues: 0 sheet: 0.19 (0.52), residues: 91 loop : -1.86 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 377 HIS 0.001 0.000 HIS A 331 PHE 0.010 0.001 PHE A 423 TYR 0.012 0.001 TYR D 486 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.228 Fit side-chains REVERT: A 340 MET cc_start: 0.8757 (mmm) cc_final: 0.8498 (mtt) REVERT: A 365 ARG cc_start: 0.8316 (mtm110) cc_final: 0.7886 (mtm110) REVERT: A 375 ARG cc_start: 0.7442 (mtp180) cc_final: 0.6741 (tpt170) REVERT: D 567 GLU cc_start: 0.7878 (OUTLIER) cc_final: 0.7530 (pt0) REVERT: D 576 GLU cc_start: 0.8559 (mt-10) cc_final: 0.8225 (mp0) outliers start: 10 outliers final: 8 residues processed: 46 average time/residue: 0.1746 time to fit residues: 9.1644 Evaluate side-chains 49 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 40 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 567 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 chunk 5 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.086641 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3296 r_free = 0.3296 target = 0.073460 restraints weight = 5985.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.075501 restraints weight = 3126.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076861 restraints weight = 2025.033| |-----------------------------------------------------------------------------| r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7860 moved from start: 0.3856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2069 Z= 0.164 Angle : 0.650 5.839 2792 Z= 0.312 Chirality : 0.046 0.226 333 Planarity : 0.003 0.037 352 Dihedral : 12.307 113.658 420 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 5.12 % Allowed : 22.33 % Favored : 72.56 % 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: -1.43 (0.50), residues: 253 helix: None (None), residues: 0 sheet: 0.27 (0.53), residues: 91 loop : -1.80 (0.45), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 377 HIS 0.003 0.001 HIS D 565 PHE 0.008 0.001 PHE A 423 TYR 0.009 0.001 TYR D 486 ARG 0.001 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.249 Fit side-chains REVERT: A 340 MET cc_start: 0.8717 (mmm) cc_final: 0.8440 (mtt) REVERT: A 365 ARG cc_start: 0.8252 (mtm110) cc_final: 0.7830 (mtm110) REVERT: A 375 ARG cc_start: 0.7363 (mtp180) cc_final: 0.6701 (tpt170) REVERT: A 431 MET cc_start: 0.8828 (mmp) cc_final: 0.8531 (mmp) REVERT: D 567 GLU cc_start: 0.7820 (OUTLIER) cc_final: 0.7477 (pt0) outliers start: 11 outliers final: 9 residues processed: 49 average time/residue: 0.1774 time to fit residues: 9.9234 Evaluate side-chains 50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 417 LEU Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 501 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 567 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 0.6980 chunk 8 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 0 optimal weight: 6.9990 chunk 18 optimal weight: 0.0570 chunk 9 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 overall best weight: 1.5302 ------------------------------------------------------------------------------- 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 = 0.3496 r_free = 0.3496 target = 0.084488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.071843 restraints weight = 6062.288| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.073788 restraints weight = 3131.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.075059 restraints weight = 2011.885| |-----------------------------------------------------------------------------| r_work (final): 0.3324 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.3901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 2069 Z= 0.265 Angle : 0.671 6.000 2792 Z= 0.329 Chirality : 0.047 0.213 333 Planarity : 0.004 0.041 352 Dihedral : 12.047 113.057 420 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 6.51 % Allowed : 22.79 % Favored : 70.70 % 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: -1.71 (0.49), residues: 253 helix: None (None), residues: 0 sheet: 0.17 (0.53), residues: 91 loop : -2.07 (0.43), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 377 HIS 0.003 0.001 HIS D 565 PHE 0.010 0.001 PHE A 423 TYR 0.020 0.002 TYR D 486 ARG 0.002 0.000 ARG A 395 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 40 time to evaluate : 0.223 Fit side-chains REVERT: A 340 MET cc_start: 0.8720 (mmm) cc_final: 0.8511 (mtt) REVERT: A 348 GLN cc_start: 0.8539 (mm-40) cc_final: 0.8318 (mm-40) REVERT: A 365 ARG cc_start: 0.8327 (mtm110) cc_final: 0.7795 (mtm110) REVERT: A 375 ARG cc_start: 0.7421 (mtp180) cc_final: 0.6731 (tpt170) REVERT: D 567 GLU cc_start: 0.7880 (OUTLIER) cc_final: 0.7533 (pt0) outliers start: 14 outliers final: 9 residues processed: 51 average time/residue: 0.1655 time to fit residues: 9.6110 Evaluate side-chains 48 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 567 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 1 optimal weight: 0.8980 chunk 15 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 14 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.086097 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.072915 restraints weight = 6119.391| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.074936 restraints weight = 3180.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3360 r_free = 0.3360 target = 0.076281 restraints weight = 2061.048| |-----------------------------------------------------------------------------| r_work (final): 0.3363 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7895 moved from start: 0.4073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2069 Z= 0.192 Angle : 0.653 5.894 2792 Z= 0.318 Chirality : 0.046 0.210 333 Planarity : 0.003 0.042 352 Dihedral : 11.655 111.156 420 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.12 % Allowed : 24.19 % Favored : 70.70 % 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: -1.66 (0.49), residues: 253 helix: None (None), residues: 0 sheet: 0.22 (0.53), residues: 91 loop : -2.04 (0.44), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 377 HIS 0.002 0.001 HIS D 565 PHE 0.009 0.001 PHE A 423 TYR 0.010 0.001 TYR D 486 ARG 0.001 0.000 ARG D 531 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.245 Fit side-chains REVERT: A 365 ARG cc_start: 0.8198 (mtm110) cc_final: 0.7798 (mtm110) REVERT: A 375 ARG cc_start: 0.7415 (mtp180) cc_final: 0.6732 (tpt170) REVERT: D 567 GLU cc_start: 0.7847 (OUTLIER) cc_final: 0.7512 (pt0) REVERT: D 576 GLU cc_start: 0.8555 (mt-10) cc_final: 0.8227 (mp0) outliers start: 11 outliers final: 9 residues processed: 47 average time/residue: 0.1823 time to fit residues: 9.7606 Evaluate side-chains 49 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain A residue 420 LYS Chi-restraints excluded: chain D residue 477 VAL Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 567 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 0.0870 chunk 2 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 chunk 0 optimal weight: 6.9990 chunk 20 optimal weight: 0.0020 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.5368 ------------------------------------------------------------------------------- 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 = 0.3531 r_free = 0.3531 target = 0.086299 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.073624 restraints weight = 6134.900| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.075564 restraints weight = 3152.394| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076875 restraints weight = 2031.054| |-----------------------------------------------------------------------------| r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.4203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2069 Z= 0.166 Angle : 0.651 6.217 2792 Z= 0.311 Chirality : 0.045 0.195 333 Planarity : 0.003 0.040 352 Dihedral : 11.416 110.405 420 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 4.19 % Allowed : 25.58 % Favored : 70.23 % 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 (0.49), residues: 253 helix: -4.02 (0.77), residues: 6 sheet: 0.11 (0.53), residues: 90 loop : -2.15 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 377 HIS 0.002 0.001 HIS D 565 PHE 0.008 0.001 PHE A 423 TYR 0.007 0.001 TYR D 486 ARG 0.001 0.000 ARG D 459 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 506 Ramachandran restraints generated. 253 Oldfield, 0 Emsley, 253 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.218 Fit side-chains REVERT: A 365 ARG cc_start: 0.8203 (mtm110) cc_final: 0.7713 (mtm110) REVERT: A 375 ARG cc_start: 0.7534 (mtp180) cc_final: 0.6771 (tpt170) REVERT: D 567 GLU cc_start: 0.7874 (OUTLIER) cc_final: 0.7508 (pt0) outliers start: 9 outliers final: 7 residues processed: 48 average time/residue: 0.1736 time to fit residues: 9.4603 Evaluate side-chains 50 residues out of total 227 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 382 THR Chi-restraints excluded: chain A residue 393 LEU Chi-restraints excluded: chain D residue 485 LEU Chi-restraints excluded: chain D residue 503 MET Chi-restraints excluded: chain D residue 504 THR Chi-restraints excluded: chain D residue 509 THR Chi-restraints excluded: chain D residue 567 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 19 optimal weight: 0.2980 chunk 18 optimal weight: 0.0010 chunk 14 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 3 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 21 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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 = 0.3551 r_free = 0.3551 target = 0.087039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.074172 restraints weight = 6054.529| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.076177 restraints weight = 3101.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3390 r_free = 0.3390 target = 0.077543 restraints weight = 1997.639| |-----------------------------------------------------------------------------| r_work (final): 0.3381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.4393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2069 Z= 0.176 Angle : 0.658 6.305 2792 Z= 0.316 Chirality : 0.045 0.184 333 Planarity : 0.003 0.037 352 Dihedral : 11.204 109.099 420 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 4.19 % Allowed : 26.05 % Favored : 69.77 % 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: -1.87 (0.49), residues: 253 helix: -3.72 (1.09), residues: 6 sheet: 0.14 (0.54), residues: 90 loop : -2.12 (0.44), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 377 HIS 0.002 0.001 HIS D 565 PHE 0.007 0.001 PHE A 423 TYR 0.008 0.001 TYR D 486 ARG 0.001 0.000 ARG A 395 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1287.67 seconds wall clock time: 23 minutes 28.81 seconds (1408.81 seconds total)