Starting phenix.real_space_refine on Wed Mar 5 14:51:33 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8x5x_38074/03_2025/8x5x_38074.cif Found real_map, /net/cci-nas-00/data/ceres_data/8x5x_38074/03_2025/8x5x_38074.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/8x5x_38074/03_2025/8x5x_38074.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8x5x_38074/03_2025/8x5x_38074.map" model { file = "/net/cci-nas-00/data/ceres_data/8x5x_38074/03_2025/8x5x_38074.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8x5x_38074/03_2025/8x5x_38074.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= -0.000 sd= 0.052 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 19 5.16 5 C 1410 2.51 5 N 339 2.21 5 O 337 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2105 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 2105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2105 Classifications: {'peptide': 256} Link IDs: {'PTRANS': 8, 'TRANS': 247} Chain breaks: 4 Time building chain proxies: 2.14, per 1000 atoms: 1.02 Number of scatterers: 2105 At special positions: 0 Unit cell: (49.22, 70.62, 72.76, 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 19 16.00 O 337 8.00 N 339 7.00 C 1410 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS B 100 " - pdb=" SG CYS B 180 " distance=2.04 Simple disulfide: pdb=" SG CYS B 441 " - pdb=" SG CYS B 444 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 220.8 milliseconds 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 496 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 0 sheets defined 85.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.24 Creating SS restraints... Processing helix chain 'B' and resid 29 through 55 removed outlier: 3.861A pdb=" N VAL B 33 " --> pdb=" O PRO B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 90 Proline residue: B 82 - end of helix removed outlier: 4.414A pdb=" N MET B 90 " --> pdb=" O LEU B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 131 Processing helix chain 'B' and resid 132 through 134 No H-bonds generated for 'chain 'B' and resid 132 through 134' Processing helix chain 'B' and resid 140 through 157 removed outlier: 3.887A pdb=" N SER B 145 " --> pdb=" O LYS B 141 " (cutoff:3.500A) removed outlier: 4.029A pdb=" N ALA B 146 " --> pdb=" O THR B 142 " (cutoff:3.500A) Processing helix chain 'B' and resid 158 through 164 removed outlier: 3.932A pdb=" N ILE B 162 " --> pdb=" O TRP B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 188 through 221 removed outlier: 5.167A pdb=" N LEU B 201 " --> pdb=" O ILE B 197 " (cutoff:3.500A) Proline residue: B 202 - end of helix Processing helix chain 'B' and resid 409 through 439 Proline residue: B 430 - end of helix Processing helix chain 'B' and resid 446 through 472 Proline residue: B 465 - end of helix Proline residue: B 469 - end of helix removed outlier: 3.797A pdb=" N ASN B 472 " --> pdb=" O TYR B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 472 through 481 removed outlier: 3.700A pdb=" N ARG B 481 " --> pdb=" O LYS B 477 " (cutoff:3.500A) 157 hydrogen bonds defined for protein. 471 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: 0.50 Time building geometry restraints manager: 0.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 608 1.35 - 1.47: 608 1.47 - 1.60: 917 1.60 - 1.72: 0 1.72 - 1.84: 29 Bond restraints: 2162 Sorted by residual: bond pdb=" C ILE B 429 " pdb=" N PRO B 430 " ideal model delta sigma weight residual 1.334 1.379 -0.045 2.34e-02 1.83e+03 3.68e+00 bond pdb=" CG1 ILE B 438 " pdb=" CD1 ILE B 438 " ideal model delta sigma weight residual 1.513 1.456 0.057 3.90e-02 6.57e+02 2.13e+00 bond pdb=" CG1 ILE B 115 " pdb=" CD1 ILE B 115 " ideal model delta sigma weight residual 1.513 1.459 0.054 3.90e-02 6.57e+02 1.91e+00 bond pdb=" CB CYS B 180 " pdb=" SG CYS B 180 " ideal model delta sigma weight residual 1.808 1.843 -0.035 3.30e-02 9.18e+02 1.15e+00 bond pdb=" N GLU B 181 " pdb=" CA GLU B 181 " ideal model delta sigma weight residual 1.468 1.455 0.013 1.24e-02 6.50e+03 1.12e+00 ... (remaining 2157 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 2797 1.60 - 3.19: 101 3.19 - 4.79: 23 4.79 - 6.38: 10 6.38 - 7.98: 2 Bond angle restraints: 2933 Sorted by residual: angle pdb=" CA TRP B 455 " pdb=" CB TRP B 455 " pdb=" CG TRP B 455 " ideal model delta sigma weight residual 113.60 118.52 -4.92 1.90e+00 2.77e-01 6.69e+00 angle pdb=" CA LEU B 39 " pdb=" CB LEU B 39 " pdb=" CG LEU B 39 " ideal model delta sigma weight residual 116.30 124.28 -7.98 3.50e+00 8.16e-02 5.20e+00 angle pdb=" C THR B 478 " pdb=" N PHE B 479 " pdb=" CA PHE B 479 " ideal model delta sigma weight residual 121.58 117.23 4.35 1.95e+00 2.63e-01 4.97e+00 angle pdb=" C LEU B 426 " pdb=" N CYS B 427 " pdb=" CA CYS B 427 " ideal model delta sigma weight residual 122.65 119.13 3.52 1.60e+00 3.91e-01 4.85e+00 angle pdb=" N GLY B 96 " pdb=" CA GLY B 96 " pdb=" C GLY B 96 " ideal model delta sigma weight residual 113.18 108.34 4.84 2.37e+00 1.78e-01 4.16e+00 ... (remaining 2928 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.23: 1104 16.23 - 32.46: 119 32.46 - 48.69: 34 48.69 - 64.91: 3 64.91 - 81.14: 3 Dihedral angle restraints: 1263 sinusoidal: 504 harmonic: 759 Sorted by residual: dihedral pdb=" CB CYS B 441 " pdb=" SG CYS B 441 " pdb=" SG CYS B 444 " pdb=" CB CYS B 444 " ideal model delta sinusoidal sigma weight residual 93.00 174.14 -81.14 1 1.00e+01 1.00e-02 8.12e+01 dihedral pdb=" SG CYS B 441 " pdb=" CB CYS B 444 " pdb=" SG CYS B 444 " pdb=" CA CYS B 444 " ideal model delta sinusoidal sigma weight residual 79.00 8.82 70.18 1 2.00e+01 2.50e-03 1.59e+01 dihedral pdb=" CA CYS B 427 " pdb=" C CYS B 427 " pdb=" N TRP B 428 " pdb=" CA TRP B 428 " ideal model delta harmonic sigma weight residual 180.00 161.55 18.45 0 5.00e+00 4.00e-02 1.36e+01 ... (remaining 1260 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 208 0.032 - 0.065: 84 0.065 - 0.097: 36 0.097 - 0.129: 10 0.129 - 0.162: 2 Chirality restraints: 340 Sorted by residual: chirality pdb=" CG LEU B 74 " pdb=" CB LEU B 74 " pdb=" CD1 LEU B 74 " pdb=" CD2 LEU B 74 " both_signs ideal model delta sigma weight residual False -2.59 -2.75 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CB VAL B 79 " pdb=" CA VAL B 79 " pdb=" CG1 VAL B 79 " pdb=" CG2 VAL B 79 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.53e-01 chirality pdb=" CA ILE B 115 " pdb=" N ILE B 115 " pdb=" C ILE B 115 " pdb=" CB ILE B 115 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 337 not shown) Planarity restraints: 344 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 455 " -0.020 2.00e-02 2.50e+03 1.56e-02 6.06e+00 pdb=" CG TRP B 455 " 0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP B 455 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TRP B 455 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 455 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 455 " -0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP B 455 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 455 " -0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 455 " 0.000 2.00e-02 2.50e+03 pdb=" CH2 TRP B 455 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP B 428 " 0.016 2.00e-02 2.50e+03 1.25e-02 3.88e+00 pdb=" CG TRP B 428 " -0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP B 428 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP B 428 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP B 428 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 428 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 428 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 428 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 428 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP B 428 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 479 " 0.013 2.00e-02 2.50e+03 1.33e-02 3.09e+00 pdb=" CG PHE B 479 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 PHE B 479 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 PHE B 479 " 0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE B 479 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 479 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 479 " 0.000 2.00e-02 2.50e+03 ... (remaining 341 not shown) Histogram of nonbonded interaction distances: 2.09 - 2.66: 18 2.66 - 3.22: 2097 3.22 - 3.78: 3431 3.78 - 4.34: 4203 4.34 - 4.90: 6642 Nonbonded interactions: 16391 Sorted by model distance: nonbonded pdb=" OD1 ASN B 63 " pdb=" OH TYR B 468 " model vdw 2.094 3.040 nonbonded pdb=" OH TYR B 65 " pdb=" OG1 THR B 147 " model vdw 2.143 3.040 nonbonded pdb=" OG1 THR B 41 " pdb=" OG1 THR B 462 " model vdw 2.277 3.040 nonbonded pdb=" O TYR B 458 " pdb=" OG SER B 461 " model vdw 2.364 3.040 nonbonded pdb=" ND2 ASN B 45 " pdb=" OD2 ASP B 73 " model vdw 2.406 3.120 ... (remaining 16386 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 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: 0.900 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: 0.020 Set scattering table: 0.020 Process input model: 10.580 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5295 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 : 0.004 0.057 2162 Z= 0.261 Angle : 0.775 7.979 2933 Z= 0.392 Chirality : 0.044 0.162 340 Planarity : 0.005 0.037 344 Dihedral : 14.147 79.862 761 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.28 % Favored : 94.72 % Rotamer: Outliers : 0.43 % Allowed : 0.43 % Favored : 99.14 % 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: 1.03 (0.56), residues: 246 helix: 1.40 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.56 (0.94), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP B 455 HIS 0.003 0.001 HIS B 450 PHE 0.031 0.002 PHE B 479 TYR 0.014 0.002 TYR B 185 ARG 0.002 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 54 time to evaluate : 0.235 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 54 average time/residue: 0.1229 time to fit residues: 7.9374 Evaluate side-chains 41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.234 ------------------------------------------------------------------------------- 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: 0.0070 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 0.7980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 84 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4644 r_free = 0.4644 target = 0.191710 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.178910 restraints weight = 4923.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4534 r_free = 0.4534 target = 0.181933 restraints weight = 2850.545| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.183985 restraints weight = 1866.614| |-----------------------------------------------------------------------------| r_work (final): 0.4560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5415 moved from start: 0.2046 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2162 Z= 0.209 Angle : 0.725 7.601 2933 Z= 0.353 Chirality : 0.042 0.136 340 Planarity : 0.004 0.043 344 Dihedral : 4.944 18.266 275 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.16 % Allowed : 10.34 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.00 (0.55), residues: 246 helix: 1.37 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -2.56 (0.96), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.002 TRP B 455 HIS 0.002 0.000 HIS B 59 PHE 0.025 0.002 PHE B 479 TYR 0.012 0.002 TYR B 126 ARG 0.001 0.000 ARG B 97 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 46 time to evaluate : 0.258 Fit side-chains revert: symmetry clash REVERT: B 185 TYR cc_start: 0.2742 (m-10) cc_final: 0.2419 (m-80) REVERT: B 454 ILE cc_start: 0.8388 (mm) cc_final: 0.8168 (mm) REVERT: B 460 ASN cc_start: 0.6684 (t0) cc_final: 0.6481 (t0) outliers start: 5 outliers final: 5 residues processed: 48 average time/residue: 0.0960 time to fit residues: 5.8981 Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 40 time to evaluate : 0.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 9.9990 chunk 7 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 5 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 45 ASN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4619 r_free = 0.4619 target = 0.188681 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4459 r_free = 0.4459 target = 0.175459 restraints weight = 4932.214| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4499 r_free = 0.4499 target = 0.178514 restraints weight = 2929.596| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.180423 restraints weight = 1950.831| |-----------------------------------------------------------------------------| r_work (final): 0.4516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5628 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 2162 Z= 0.259 Angle : 0.738 7.925 2933 Z= 0.366 Chirality : 0.043 0.123 340 Planarity : 0.005 0.047 344 Dihedral : 4.837 15.888 275 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.31 % Allowed : 16.38 % Favored : 79.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.96 (0.54), residues: 246 helix: 1.32 (0.36), residues: 200 sheet: None (None), residues: 0 loop : -2.39 (0.89), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP B 455 HIS 0.006 0.002 HIS B 167 PHE 0.023 0.002 PHE B 479 TYR 0.013 0.002 TYR B 468 ARG 0.002 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.276 Fit side-chains REVERT: B 451 MET cc_start: 0.5693 (mmt) cc_final: 0.5491 (mmt) outliers start: 10 outliers final: 7 residues processed: 45 average time/residue: 0.1072 time to fit residues: 6.0732 Evaluate side-chains 40 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 33 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 79 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 3 optimal weight: 0.2980 chunk 5 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 9 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.190424 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.177113 restraints weight = 4825.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.180138 restraints weight = 2844.759| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4536 r_free = 0.4536 target = 0.182038 restraints weight = 1898.106| |-----------------------------------------------------------------------------| r_work (final): 0.4527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5570 moved from start: 0.3407 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2162 Z= 0.206 Angle : 0.710 7.482 2933 Z= 0.344 Chirality : 0.041 0.121 340 Planarity : 0.004 0.044 344 Dihedral : 4.701 15.514 275 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 13.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 4.74 % Allowed : 21.55 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.93 (0.54), residues: 246 helix: 1.24 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -2.17 (0.89), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 455 HIS 0.002 0.001 HIS B 59 PHE 0.038 0.002 PHE B 184 TYR 0.016 0.002 TYR B 458 ARG 0.001 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 38 time to evaluate : 0.259 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 43 average time/residue: 0.0950 time to fit residues: 5.2542 Evaluate side-chains 40 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 204 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 2.9990 chunk 18 optimal weight: 0.9990 chunk 4 optimal weight: 0.7980 chunk 20 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 8 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: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 472 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4614 r_free = 0.4614 target = 0.189262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4455 r_free = 0.4455 target = 0.175333 restraints weight = 4968.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.4493 r_free = 0.4493 target = 0.178224 restraints weight = 3056.818| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.180169 restraints weight = 2115.643| |-----------------------------------------------------------------------------| r_work (final): 0.4514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5648 moved from start: 0.3810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2162 Z= 0.211 Angle : 0.692 7.561 2933 Z= 0.337 Chirality : 0.041 0.117 340 Planarity : 0.005 0.047 344 Dihedral : 4.645 17.698 275 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 13.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 5.17 % Allowed : 22.41 % Favored : 72.41 % 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: 1.08 (0.53), residues: 246 helix: 1.37 (0.36), residues: 201 sheet: None (None), residues: 0 loop : -2.27 (0.84), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.027 0.002 PHE B 479 TYR 0.013 0.002 TYR B 458 ARG 0.001 0.000 ARG B 176 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 33 time to evaluate : 0.243 Fit side-chains REVERT: B 93 TRP cc_start: 0.5332 (OUTLIER) cc_final: 0.4446 (m-10) REVERT: B 126 TYR cc_start: 0.5354 (OUTLIER) cc_final: 0.4918 (t80) REVERT: B 450 HIS cc_start: 0.6696 (OUTLIER) cc_final: 0.6179 (t-90) outliers start: 12 outliers final: 5 residues processed: 42 average time/residue: 0.0908 time to fit residues: 4.9371 Evaluate side-chains 40 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 32 time to evaluate : 0.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 204 LEU Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.5980 chunk 22 optimal weight: 0.8980 chunk 14 optimal weight: 0.1980 chunk 1 optimal weight: 0.7980 chunk 9 optimal weight: 2.9990 chunk 11 optimal weight: 9.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.189367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4451 r_free = 0.4451 target = 0.175395 restraints weight = 5017.206| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4486 r_free = 0.4486 target = 0.178217 restraints weight = 3071.063| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4514 r_free = 0.4514 target = 0.180408 restraints weight = 2151.986| |-----------------------------------------------------------------------------| r_work (final): 0.4515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5622 moved from start: 0.3936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2162 Z= 0.189 Angle : 0.685 7.748 2933 Z= 0.327 Chirality : 0.039 0.111 340 Planarity : 0.004 0.046 344 Dihedral : 4.614 16.489 275 Min Nonbonded Distance : 2.636 Molprobity Statistics. All-atom Clashscore : 11.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 6.03 % Allowed : 23.28 % Favored : 70.69 % 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: 1.11 (0.54), residues: 246 helix: 1.41 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.25 (0.87), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.024 0.001 PHE B 479 TYR 0.012 0.001 TYR B 458 ARG 0.001 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.275 Fit side-chains REVERT: B 93 TRP cc_start: 0.5244 (OUTLIER) cc_final: 0.4648 (m-10) REVERT: B 126 TYR cc_start: 0.5306 (OUTLIER) cc_final: 0.4870 (t80) REVERT: B 185 TYR cc_start: 0.2919 (m-10) cc_final: 0.2629 (m-80) REVERT: B 189 TRP cc_start: 0.4725 (OUTLIER) cc_final: 0.3157 (p-90) REVERT: B 450 HIS cc_start: 0.6672 (OUTLIER) cc_final: 0.6174 (t-90) outliers start: 14 outliers final: 6 residues processed: 43 average time/residue: 0.0982 time to fit residues: 5.4281 Evaluate side-chains 42 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.276 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 LEU Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 8.9990 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 10 optimal weight: 0.1980 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 130 GLN ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4603 r_free = 0.4603 target = 0.189051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.175313 restraints weight = 5090.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4489 r_free = 0.4489 target = 0.178319 restraints weight = 3018.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.180157 restraints weight = 2048.850| |-----------------------------------------------------------------------------| r_work (final): 0.4509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5628 moved from start: 0.4175 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2162 Z= 0.184 Angle : 0.658 7.260 2933 Z= 0.316 Chirality : 0.039 0.113 340 Planarity : 0.004 0.048 344 Dihedral : 4.692 16.556 275 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.74 % Allowed : 24.14 % Favored : 71.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.36 (0.54), residues: 246 helix: 1.57 (0.37), residues: 200 sheet: None (None), residues: 0 loop : -2.12 (0.88), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.024 0.001 PHE B 479 TYR 0.010 0.001 TYR B 458 ARG 0.001 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 32 time to evaluate : 0.250 Fit side-chains REVERT: B 93 TRP cc_start: 0.5310 (OUTLIER) cc_final: 0.4751 (m-10) REVERT: B 101 LEU cc_start: 0.7325 (OUTLIER) cc_final: 0.7108 (mt) REVERT: B 126 TYR cc_start: 0.5304 (OUTLIER) cc_final: 0.4811 (t80) REVERT: B 189 TRP cc_start: 0.4639 (OUTLIER) cc_final: 0.3040 (p-90) REVERT: B 442 LYS cc_start: 0.6643 (mmmt) cc_final: 0.6356 (tptp) REVERT: B 450 HIS cc_start: 0.6542 (OUTLIER) cc_final: 0.6125 (t-90) outliers start: 11 outliers final: 6 residues processed: 42 average time/residue: 0.1157 time to fit residues: 6.1011 Evaluate side-chains 42 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 31 time to evaluate : 0.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 101 LEU Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.0770 chunk 20 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.188226 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.174662 restraints weight = 5065.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4484 r_free = 0.4484 target = 0.177576 restraints weight = 2984.933| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.179733 restraints weight = 2036.926| |-----------------------------------------------------------------------------| r_work (final): 0.4503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.4403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 2162 Z= 0.191 Angle : 0.671 7.325 2933 Z= 0.323 Chirality : 0.039 0.114 340 Planarity : 0.004 0.047 344 Dihedral : 4.707 16.837 275 Min Nonbonded Distance : 2.644 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.31 % Allowed : 25.86 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.54), residues: 246 helix: 1.44 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.02 (0.88), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 189 HIS 0.003 0.001 HIS B 167 PHE 0.023 0.001 PHE B 479 TYR 0.010 0.001 TYR B 458 ARG 0.001 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 32 time to evaluate : 0.269 Fit side-chains revert: symmetry clash REVERT: B 126 TYR cc_start: 0.5372 (OUTLIER) cc_final: 0.4877 (t80) REVERT: B 189 TRP cc_start: 0.4426 (OUTLIER) cc_final: 0.2816 (p-90) REVERT: B 450 HIS cc_start: 0.6528 (OUTLIER) cc_final: 0.6215 (t-90) outliers start: 10 outliers final: 6 residues processed: 40 average time/residue: 0.1081 time to fit residues: 5.4577 Evaluate side-chains 39 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 30 time to evaluate : 0.252 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 23 optimal weight: 0.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 6 optimal weight: 0.0970 chunk 0 optimal weight: 7.9990 chunk 4 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 4.9990 chunk 18 optimal weight: 0.0040 overall best weight: 0.5590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4627 r_free = 0.4627 target = 0.191037 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.179105 restraints weight = 5310.590| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.181279 restraints weight = 3543.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.182640 restraints weight = 2594.839| |-----------------------------------------------------------------------------| r_work (final): 0.4491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5655 moved from start: 0.4646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2162 Z= 0.183 Angle : 0.676 7.214 2933 Z= 0.326 Chirality : 0.039 0.112 340 Planarity : 0.004 0.048 344 Dihedral : 4.717 16.918 275 Min Nonbonded Distance : 2.629 Molprobity Statistics. All-atom Clashscore : 10.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 4.74 % Allowed : 25.43 % Favored : 69.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.55), residues: 246 helix: 1.52 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -1.94 (0.89), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.039 0.002 PHE B 475 TYR 0.029 0.002 TYR B 185 ARG 0.001 0.000 ARG B 53 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.239 Fit side-chains REVERT: B 93 TRP cc_start: 0.5353 (OUTLIER) cc_final: 0.4988 (m-10) REVERT: B 126 TYR cc_start: 0.5289 (OUTLIER) cc_final: 0.4811 (t80) REVERT: B 189 TRP cc_start: 0.4448 (OUTLIER) cc_final: 0.2842 (p-90) REVERT: B 450 HIS cc_start: 0.6466 (OUTLIER) cc_final: 0.6180 (t-90) outliers start: 11 outliers final: 7 residues processed: 37 average time/residue: 0.1162 time to fit residues: 5.4232 Evaluate side-chains 40 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 29 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.0980 chunk 8 optimal weight: 0.9980 chunk 22 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 6 optimal weight: 4.9990 chunk 7 optimal weight: 0.8980 chunk 13 optimal weight: 5.9990 chunk 16 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4620 r_free = 0.4620 target = 0.190774 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4485 r_free = 0.4485 target = 0.179101 restraints weight = 5321.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4508 r_free = 0.4508 target = 0.181205 restraints weight = 3486.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.182746 restraints weight = 2538.366| |-----------------------------------------------------------------------------| r_work (final): 0.4528 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5622 moved from start: 0.4753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 2162 Z= 0.195 Angle : 0.724 9.006 2933 Z= 0.346 Chirality : 0.040 0.155 340 Planarity : 0.004 0.048 344 Dihedral : 4.735 16.873 275 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 10.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.07 % Favored : 95.93 % Rotamer: Outliers : 4.74 % Allowed : 26.72 % Favored : 68.53 % 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: 1.16 (0.55), residues: 246 helix: 1.40 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.07 (0.88), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP B 455 HIS 0.002 0.001 HIS B 167 PHE 0.039 0.002 PHE B 475 TYR 0.028 0.002 TYR B 185 ARG 0.001 0.000 ARG B 53 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 492 Ramachandran restraints generated. 246 Oldfield, 0 Emsley, 246 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.255 Fit side-chains REVERT: B 93 TRP cc_start: 0.5463 (OUTLIER) cc_final: 0.5107 (m-10) REVERT: B 126 TYR cc_start: 0.5366 (OUTLIER) cc_final: 0.4882 (t80) REVERT: B 189 TRP cc_start: 0.4389 (OUTLIER) cc_final: 0.2789 (p-90) REVERT: B 450 HIS cc_start: 0.6331 (OUTLIER) cc_final: 0.6000 (t-90) REVERT: B 461 SER cc_start: 0.7723 (t) cc_final: 0.7469 (p) outliers start: 11 outliers final: 7 residues processed: 38 average time/residue: 0.1181 time to fit residues: 5.5742 Evaluate side-chains 41 residues out of total 232 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 30 time to evaluate : 0.231 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 71 VAL Chi-restraints excluded: chain B residue 93 TRP Chi-restraints excluded: chain B residue 104 LEU Chi-restraints excluded: chain B residue 115 ILE Chi-restraints excluded: chain B residue 126 TYR Chi-restraints excluded: chain B residue 154 LEU Chi-restraints excluded: chain B residue 189 TRP Chi-restraints excluded: chain B residue 197 ILE Chi-restraints excluded: chain B residue 435 PHE Chi-restraints excluded: chain B residue 442 LYS Chi-restraints excluded: chain B residue 450 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 12 optimal weight: 0.3980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.0070 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.0870 chunk 13 optimal weight: 0.7980 chunk 14 optimal weight: 0.0020 overall best weight: 0.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 460 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4637 r_free = 0.4637 target = 0.191969 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.180468 restraints weight = 5344.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4530 r_free = 0.4530 target = 0.182651 restraints weight = 3473.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4546 r_free = 0.4546 target = 0.184126 restraints weight = 2497.480| |-----------------------------------------------------------------------------| r_work (final): 0.4508 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5577 moved from start: 0.4761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 2162 Z= 0.177 Angle : 0.712 11.039 2933 Z= 0.336 Chirality : 0.040 0.161 340 Planarity : 0.004 0.050 344 Dihedral : 4.637 16.948 275 Min Nonbonded Distance : 2.645 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 4.31 % Allowed : 26.72 % Favored : 68.97 % 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: 1.30 (0.55), residues: 246 helix: 1.51 (0.37), residues: 201 sheet: None (None), residues: 0 loop : -2.09 (0.88), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 455 HIS 0.002 0.001 HIS B 59 PHE 0.035 0.002 PHE B 475 TYR 0.027 0.002 TYR B 185 ARG 0.001 0.000 ARG B 409 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1173.00 seconds wall clock time: 20 minutes 57.39 seconds (1257.39 seconds total)