Starting phenix.real_space_refine on Thu Jan 16 12:06:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bit_44601/01_2025/9bit_44601_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bit_44601/01_2025/9bit_44601.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bit_44601/01_2025/9bit_44601.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bit_44601/01_2025/9bit_44601.map" model { file = "/net/cci-nas-00/data/ceres_data/9bit_44601/01_2025/9bit_44601_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bit_44601/01_2025/9bit_44601_trim.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.046 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians S 34 5.16 5 Cl 1 4.86 5 C 3101 2.51 5 N 767 2.21 5 O 811 1.98 5 H 4734 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5571/modules/chem_data/mon_lib" Total number of atoms: 9448 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 7529 Number of conformers: 1 Conformer: "" Number of residues, atoms: 472, 7529 Classifications: {'peptide': 472} Link IDs: {'PTRANS': 21, 'TRANS': 450} Chain breaks: 1 Chain: "B" Number of atoms: 1890 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 1890 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 4, 'TRANS': 118} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'CXN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.10, per 1000 atoms: 0.65 Number of scatterers: 9448 At special positions: 0 Unit cell: (87.108, 109.8, 83.448, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 34 16.00 O 811 8.00 N 767 7.00 C 3101 6.00 H 4734 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 211 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 96 " 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: 2.45 Conformation dependent library (CDL) restraints added in 597.4 milliseconds 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 24 helices and 2 sheets defined 64.0% alpha, 6.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'A' and resid 43 through 45 No H-bonds generated for 'chain 'A' and resid 43 through 45' Processing helix chain 'A' and resid 46 through 74 removed outlier: 5.106A pdb=" N ASN A 52 " --> pdb=" O PHE A 48 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N VAL A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) removed outlier: 4.409A pdb=" N THR A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 4.843A pdb=" N LEU A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) Processing helix chain 'A' and resid 78 through 96 Processing helix chain 'A' and resid 96 through 107 Processing helix chain 'A' and resid 112 through 132 removed outlier: 3.534A pdb=" N ALA A 132 " --> pdb=" O LYS A 128 " (cutoff:3.500A) Processing helix chain 'A' and resid 140 through 171 removed outlier: 4.234A pdb=" N GLY A 159 " --> pdb=" O LEU A 155 " (cutoff:3.500A) Proline residue: A 162 - end of helix removed outlier: 3.790A pdb=" N ALA A 165 " --> pdb=" O LYS A 161 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N GLN A 171 " --> pdb=" O PHE A 167 " (cutoff:3.500A) Processing helix chain 'A' and resid 176 through 206 removed outlier: 3.573A pdb=" N ARG A 180 " --> pdb=" O HIS A 176 " (cutoff:3.500A) removed outlier: 3.888A pdb=" N THR A 181 " --> pdb=" O ALA A 177 " (cutoff:3.500A) removed outlier: 3.664A pdb=" N ARG A 182 " --> pdb=" O GLU A 178 " (cutoff:3.500A) Proline residue: A 203 - end of helix removed outlier: 3.590A pdb=" N ARG A 206 " --> pdb=" O THR A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 216 through 238 removed outlier: 3.971A pdb=" N ALA A 220 " --> pdb=" O CYS A 216 " (cutoff:3.500A) Proline residue: A 224 - end of helix removed outlier: 3.710A pdb=" N GLY A 238 " --> pdb=" O VAL A 234 " (cutoff:3.500A) Processing helix chain 'A' and resid 239 through 242 Processing helix chain 'A' and resid 250 through 266 removed outlier: 3.870A pdb=" N ARG A 266 " --> pdb=" O ALA A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 289 through 307 removed outlier: 3.974A pdb=" N ASP A 295 " --> pdb=" O HIS A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 318 removed outlier: 3.674A pdb=" N PHE A 312 " --> pdb=" O PRO A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.595A pdb=" N LEU A 325 " --> pdb=" O SER A 321 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 329 " --> pdb=" O LEU A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 345 Processing helix chain 'A' and resid 346 through 362 removed outlier: 3.576A pdb=" N PHE A 350 " --> pdb=" O VAL A 346 " (cutoff:3.500A) Proline residue: A 357 - end of helix Processing helix chain 'A' and resid 362 through 370 removed outlier: 3.913A pdb=" N CYS A 370 " --> pdb=" O LEU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 377 through 403 Processing helix chain 'A' and resid 611 through 636 removed outlier: 3.532A pdb=" N GLU A 631 " --> pdb=" O VAL A 627 " (cutoff:3.500A) Processing helix chain 'A' and resid 638 through 642 removed outlier: 3.887A pdb=" N LYS A 642 " --> pdb=" O SER A 639 " (cutoff:3.500A) Processing helix chain 'A' and resid 643 through 665 removed outlier: 3.794A pdb=" N VAL A 653 " --> pdb=" O TRP A 649 " (cutoff:3.500A) removed outlier: 4.249A pdb=" N GLN A 665 " --> pdb=" O LEU A 661 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 695 Processing helix chain 'B' and resid 28 through 30 No H-bonds generated for 'chain 'B' and resid 28 through 30' Processing helix chain 'B' and resid 53 through 56 removed outlier: 4.209A pdb=" N ARG B 56 " --> pdb=" O TRP B 53 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 53 through 56' Processing helix chain 'B' and resid 110 through 114 Processing sheet with id=AA1, first strand: chain 'B' and resid 18 through 23 Processing sheet with id=AA2, first strand: chain 'B' and resid 58 through 60 removed outlier: 5.308A pdb=" N PHE B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N ARG B 38 " --> pdb=" O PHE B 47 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N CYS B 96 " --> pdb=" O GLY B 118 " (cutoff:3.500A) 281 hydrogen bonds defined for protein. 810 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: 3.30 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 4724 1.04 - 1.24: 632 1.24 - 1.44: 1489 1.44 - 1.64: 2676 1.64 - 1.84: 55 Bond restraints: 9576 Sorted by residual: bond pdb=" C ALA A 104 " pdb=" N ASP A 105 " ideal model delta sigma weight residual 1.335 1.287 0.048 1.36e-02 5.41e+03 1.26e+01 bond pdb=" N25 CXN A 801 " pdb=" O24 CXN A 801 " ideal model delta sigma weight residual 1.363 1.416 -0.053 2.00e-02 2.50e+03 7.05e+00 bond pdb=" N ASP A 105 " pdb=" H ASP A 105 " ideal model delta sigma weight residual 0.860 0.912 -0.052 2.00e-02 2.50e+03 6.70e+00 bond pdb=" C6 CXN A 801 " pdb=" C8 CXN A 801 " ideal model delta sigma weight residual 1.546 1.507 0.039 2.00e-02 2.50e+03 3.80e+00 bond pdb=" C ASP A 105 " pdb=" O ASP A 105 " ideal model delta sigma weight residual 1.237 1.214 0.023 1.19e-02 7.06e+03 3.61e+00 ... (remaining 9571 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 17141 1.97 - 3.94: 138 3.94 - 5.91: 12 5.91 - 7.88: 0 7.88 - 9.84: 2 Bond angle restraints: 17293 Sorted by residual: angle pdb=" CA ASP A 105 " pdb=" C ASP A 105 " pdb=" O ASP A 105 " ideal model delta sigma weight residual 120.42 116.81 3.61 1.06e+00 8.90e-01 1.16e+01 angle pdb=" C21 CXN A 801 " pdb=" C22 CXN A 801 " pdb=" C26 CXN A 801 " ideal model delta sigma weight residual 132.03 122.19 9.84 3.00e+00 1.11e-01 1.08e+01 angle pdb=" C ALA A 104 " pdb=" N ASP A 105 " pdb=" CA ASP A 105 " ideal model delta sigma weight residual 120.29 124.57 -4.28 1.42e+00 4.96e-01 9.10e+00 angle pdb=" C21 CXN A 801 " pdb=" C22 CXN A 801 " pdb=" C23 CXN A 801 " ideal model delta sigma weight residual 124.59 133.26 -8.67 3.00e+00 1.11e-01 8.35e+00 angle pdb=" N THR A 96 " pdb=" CA THR A 96 " pdb=" C THR A 96 " ideal model delta sigma weight residual 109.81 115.47 -5.66 2.21e+00 2.05e-01 6.57e+00 ... (remaining 17288 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.03: 4246 27.03 - 54.06: 244 54.06 - 81.08: 44 81.08 - 108.11: 3 108.11 - 135.14: 4 Dihedral angle restraints: 4541 sinusoidal: 2402 harmonic: 2139 Sorted by residual: dihedral pdb=" CA TRP A 283 " pdb=" C TRP A 283 " pdb=" N ALA A 284 " pdb=" CA ALA A 284 " ideal model delta harmonic sigma weight residual 180.00 157.35 22.65 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" CA GLY A 159 " pdb=" C GLY A 159 " pdb=" N ILE A 160 " pdb=" CA ILE A 160 " ideal model delta harmonic sigma weight residual 180.00 157.36 22.64 0 5.00e+00 4.00e-02 2.05e+01 dihedral pdb=" C52 CXN A 801 " pdb=" C5 CXN A 801 " pdb=" C6 CXN A 801 " pdb=" N7 CXN A 801 " ideal model delta sinusoidal sigma weight residual 144.67 -80.19 -135.14 1 3.00e+01 1.11e-03 1.82e+01 ... (remaining 4538 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 484 0.029 - 0.057: 168 0.057 - 0.086: 57 0.086 - 0.114: 21 0.114 - 0.143: 8 Chirality restraints: 738 Sorted by residual: chirality pdb=" CA ILE A 133 " pdb=" N ILE A 133 " pdb=" C ILE A 133 " pdb=" CB ILE A 133 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.11e-01 chirality pdb=" CA PRO A 97 " pdb=" N PRO A 97 " pdb=" C PRO A 97 " pdb=" CB PRO A 97 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.12e-01 chirality pdb=" CA ILE A 601 " pdb=" N ILE A 601 " pdb=" C ILE A 601 " pdb=" CB ILE A 601 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.96e-01 ... (remaining 735 not shown) Planarity restraints: 1381 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 CXN A 801 " 0.191 2.00e-02 2.50e+03 1.65e-01 3.41e+02 pdb=" C21 CXN A 801 " -0.042 2.00e-02 2.50e+03 pdb=" C22 CXN A 801 " -0.028 2.00e-02 2.50e+03 pdb=" N2 CXN A 801 " -0.273 2.00e-02 2.50e+03 pdb=" O21 CXN A 801 " 0.151 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C21 CXN A 801 " 0.050 2.00e-02 2.50e+03 3.67e-02 2.70e+01 pdb=" C22 CXN A 801 " -0.015 2.00e-02 2.50e+03 pdb=" C23 CXN A 801 " 0.016 2.00e-02 2.50e+03 pdb=" C26 CXN A 801 " -0.010 2.00e-02 2.50e+03 pdb=" C27 CXN A 801 " -0.058 2.00e-02 2.50e+03 pdb=" C28 CXN A 801 " -0.046 2.00e-02 2.50e+03 pdb=" N25 CXN A 801 " 0.023 2.00e-02 2.50e+03 pdb=" O24 CXN A 801 " 0.040 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL B 87 " 0.032 5.00e-02 4.00e+02 4.87e-02 3.79e+00 pdb=" N PRO B 88 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO B 88 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO B 88 " 0.027 5.00e-02 4.00e+02 ... (remaining 1378 not shown) Histogram of nonbonded interaction distances: 1.64 - 2.23: 1029 2.23 - 2.83: 20711 2.83 - 3.42: 24832 3.42 - 4.01: 33869 4.01 - 4.60: 52356 Nonbonded interactions: 132797 Sorted by model distance: nonbonded pdb=" O TRP B 53 " pdb=" HG SER B 54 " model vdw 1.642 2.450 nonbonded pdb=" O ALA A 637 " pdb=" HZ3 LYS A 642 " model vdw 1.659 2.450 nonbonded pdb=" OD1 ASP A 170 " pdb=" HH TYR A 634 " model vdw 1.670 2.450 nonbonded pdb=" O PHE A 167 " pdb="HE21 GLN A 171 " model vdw 1.676 2.450 nonbonded pdb=" OD1 ASP A 333 " pdb=" H LEU A 334 " model vdw 1.678 2.450 ... (remaining 132792 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.680 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: 0.170 Extract box with map and model: 0.350 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 24.370 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.620 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8164 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 : 0.003 0.053 4842 Z= 0.191 Angle : 0.603 9.844 6583 Z= 0.321 Chirality : 0.037 0.143 738 Planarity : 0.007 0.165 814 Dihedral : 18.476 135.140 1725 Min Nonbonded Distance : 2.073 Molprobity Statistics. All-atom Clashscore : 6.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.60 % Allowed : 24.40 % Favored : 74.00 % 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: -0.05 (0.36), residues: 589 helix: 1.20 (0.29), residues: 343 sheet: -1.84 (0.65), residues: 59 loop : -1.72 (0.45), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.008 0.001 PHE A 48 TYR 0.010 0.001 TYR A 183 ARG 0.002 0.000 ARG B 101 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 72 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 343 GLN cc_start: 0.7524 (mm-40) cc_final: 0.7198 (mt0) outliers start: 8 outliers final: 7 residues processed: 79 average time/residue: 0.3426 time to fit residues: 35.1472 Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 346 VAL Chi-restraints excluded: chain A residue 370 CYS Chi-restraints excluded: chain A residue 376 SER Chi-restraints excluded: chain A residue 607 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 17 optimal weight: 0.0060 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 0.9990 chunk 53 optimal weight: 0.0970 overall best weight: 0.5394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3852 r_free = 0.3852 target = 0.165023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3528 r_free = 0.3528 target = 0.137987 restraints weight = 14859.720| |-----------------------------------------------------------------------------| r_work (start): 0.3540 rms_B_bonded: 1.60 r_work: 0.3378 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3256 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3256 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.0611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4842 Z= 0.205 Angle : 0.567 5.550 6583 Z= 0.297 Chirality : 0.038 0.153 738 Planarity : 0.004 0.047 814 Dihedral : 11.775 131.184 687 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.79 % Favored : 93.21 % Rotamer: Outliers : 1.80 % Allowed : 24.20 % Favored : 74.00 % 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: 0.23 (0.36), residues: 589 helix: 1.58 (0.28), residues: 345 sheet: -2.23 (0.61), residues: 59 loop : -1.78 (0.45), residues: 185 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.017 0.001 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.004 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7280 (pm20) outliers start: 9 outliers final: 7 residues processed: 69 average time/residue: 0.3480 time to fit residues: 31.3951 Evaluate side-chains 71 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 63 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 276 LYS Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 38 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 48 optimal weight: 0.4980 chunk 18 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 41 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.163039 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3502 r_free = 0.3502 target = 0.135798 restraints weight = 15019.997| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 1.62 r_work: 0.3328 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3199 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.0876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4842 Z= 0.255 Angle : 0.574 5.338 6583 Z= 0.300 Chirality : 0.039 0.150 738 Planarity : 0.005 0.052 814 Dihedral : 11.664 139.422 680 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.47 % Favored : 92.53 % Rotamer: Outliers : 2.00 % Allowed : 23.60 % Favored : 74.40 % 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: 0.18 (0.35), residues: 589 helix: 1.56 (0.28), residues: 346 sheet: -2.07 (0.63), residues: 57 loop : -1.95 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.022 0.001 PHE A 48 TYR 0.014 0.001 TYR A 634 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.664 Fit side-chains revert: symmetry clash REVERT: B 112 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7286 (pm20) outliers start: 10 outliers final: 7 residues processed: 72 average time/residue: 0.3343 time to fit residues: 31.3578 Evaluate side-chains 72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 36 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 46 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.163228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.136210 restraints weight = 14831.958| |-----------------------------------------------------------------------------| r_work (start): 0.3497 rms_B_bonded: 1.60 r_work: 0.3340 rms_B_bonded: 2.41 restraints_weight: 0.5000 r_work: 0.3218 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3218 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8380 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4842 Z= 0.241 Angle : 0.560 5.133 6583 Z= 0.294 Chirality : 0.039 0.149 738 Planarity : 0.004 0.049 814 Dihedral : 11.338 137.111 676 Min Nonbonded Distance : 2.291 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.20 % Allowed : 23.60 % Favored : 74.20 % 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: 0.21 (0.35), residues: 589 helix: 1.61 (0.28), residues: 346 sheet: -2.11 (0.63), residues: 57 loop : -1.97 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.009 0.001 HIS A 291 PHE 0.020 0.001 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.003 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 61 time to evaluate : 0.766 Fit side-chains revert: symmetry clash REVERT: A 266 ARG cc_start: 0.6441 (OUTLIER) cc_final: 0.5728 (mtt-85) REVERT: B 112 GLU cc_start: 0.7811 (OUTLIER) cc_final: 0.7304 (pm20) outliers start: 11 outliers final: 7 residues processed: 67 average time/residue: 0.3803 time to fit residues: 32.8942 Evaluate side-chains 70 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 266 ARG Chi-restraints excluded: chain A residue 330 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 32 optimal weight: 0.0970 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 56 optimal weight: 0.9980 chunk 55 optimal weight: 1.9990 chunk 20 optimal weight: 0.0370 chunk 31 optimal weight: 0.7980 chunk 42 optimal weight: 0.9990 chunk 27 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 49 optimal weight: 0.8980 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3845 r_free = 0.3845 target = 0.164630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.137630 restraints weight = 14835.888| |-----------------------------------------------------------------------------| r_work (start): 0.3523 rms_B_bonded: 1.62 r_work: 0.3352 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3229 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3229 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.1139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4842 Z= 0.183 Angle : 0.530 4.847 6583 Z= 0.278 Chirality : 0.037 0.148 738 Planarity : 0.004 0.045 814 Dihedral : 11.254 135.995 676 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 4.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.40 % Allowed : 22.80 % Favored : 74.80 % 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: 0.41 (0.36), residues: 589 helix: 1.75 (0.28), residues: 348 sheet: -1.99 (0.64), residues: 57 loop : -1.92 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.001 0.000 HIS A 291 PHE 0.016 0.001 PHE A 48 TYR 0.011 0.001 TYR A 634 ARG 0.002 0.000 ARG A 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8495 (OUTLIER) cc_final: 0.8112 (mmm) REVERT: B 45 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8057 (ttp-170) REVERT: B 112 GLU cc_start: 0.7768 (OUTLIER) cc_final: 0.7270 (pm20) outliers start: 12 outliers final: 7 residues processed: 71 average time/residue: 0.3794 time to fit residues: 34.5401 Evaluate side-chains 72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.729 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 36 optimal weight: 0.9980 chunk 43 optimal weight: 0.7980 chunk 41 optimal weight: 0.4980 chunk 22 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 45 optimal weight: 0.9990 chunk 48 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 38 optimal weight: 0.2980 chunk 3 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 331 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.137976 restraints weight = 14885.895| |-----------------------------------------------------------------------------| r_work (start): 0.3528 rms_B_bonded: 1.61 r_work: 0.3360 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3222 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.3222 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4842 Z= 0.188 Angle : 0.531 4.895 6583 Z= 0.279 Chirality : 0.037 0.148 738 Planarity : 0.004 0.046 814 Dihedral : 11.243 136.099 676 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer: Outliers : 2.80 % Allowed : 22.60 % Favored : 74.60 % 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: 0.44 (0.36), residues: 589 helix: 1.77 (0.28), residues: 348 sheet: -1.95 (0.64), residues: 57 loop : -1.89 (0.44), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 291 PHE 0.016 0.001 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.008 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 62 time to evaluate : 0.653 Fit side-chains revert: symmetry clash REVERT: B 45 ARG cc_start: 0.8320 (OUTLIER) cc_final: 0.8040 (ttp-170) REVERT: B 73 ASP cc_start: 0.6273 (p0) cc_final: 0.6073 (p0) REVERT: B 112 GLU cc_start: 0.7796 (OUTLIER) cc_final: 0.7294 (pm20) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.3454 time to fit residues: 32.4781 Evaluate side-chains 72 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 45 ARG Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 1 optimal weight: 0.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.3980 chunk 57 optimal weight: 0.2980 chunk 15 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 52 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 0.0980 chunk 33 optimal weight: 0.2980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 = 0.3867 r_free = 0.3867 target = 0.166649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3538 r_free = 0.3538 target = 0.138788 restraints weight = 14938.257| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 1.68 r_work: 0.3369 rms_B_bonded: 2.43 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4842 Z= 0.149 Angle : 0.507 4.710 6583 Z= 0.266 Chirality : 0.037 0.147 738 Planarity : 0.004 0.046 814 Dihedral : 11.157 134.793 676 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 4.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.40 % Allowed : 22.80 % Favored : 74.80 % 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: 0.65 (0.36), residues: 589 helix: 1.99 (0.28), residues: 345 sheet: -1.82 (0.66), residues: 57 loop : -1.87 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 280 HIS 0.002 0.000 HIS A 291 PHE 0.012 0.001 PHE A 48 TYR 0.010 0.001 TYR A 634 ARG 0.006 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 61 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8482 (OUTLIER) cc_final: 0.8092 (mmm) REVERT: B 112 GLU cc_start: 0.7745 (OUTLIER) cc_final: 0.7247 (pm20) outliers start: 12 outliers final: 8 residues processed: 68 average time/residue: 0.3554 time to fit residues: 31.3563 Evaluate side-chains 70 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 46 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3825 r_free = 0.3825 target = 0.162816 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.135481 restraints weight = 15191.146| |-----------------------------------------------------------------------------| r_work (start): 0.3509 rms_B_bonded: 1.63 r_work: 0.3350 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3220 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3220 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.1375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4842 Z= 0.267 Angle : 0.560 5.175 6583 Z= 0.296 Chirality : 0.039 0.150 738 Planarity : 0.005 0.046 814 Dihedral : 11.266 136.776 676 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.40 % Allowed : 22.00 % Favored : 75.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.36), residues: 589 helix: 1.71 (0.28), residues: 346 sheet: -1.97 (0.64), residues: 57 loop : -1.89 (0.44), residues: 186 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 291 PHE 0.020 0.002 PHE A 48 TYR 0.014 0.001 TYR A 634 ARG 0.007 0.001 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 65 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8518 (OUTLIER) cc_final: 0.8172 (mmm) REVERT: B 112 GLU cc_start: 0.7828 (OUTLIER) cc_final: 0.7314 (pm20) outliers start: 12 outliers final: 9 residues processed: 71 average time/residue: 0.3434 time to fit residues: 31.6962 Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.632 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 4 optimal weight: 0.5980 chunk 0 optimal weight: 0.9990 chunk 37 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.0970 chunk 33 optimal weight: 0.6980 chunk 51 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 47 optimal weight: 0.7980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.164939 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3525 r_free = 0.3525 target = 0.137883 restraints weight = 14834.795| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 1.61 r_work: 0.3355 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.05 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4842 Z= 0.181 Angle : 0.529 4.913 6583 Z= 0.278 Chirality : 0.037 0.149 738 Planarity : 0.004 0.045 814 Dihedral : 11.206 134.679 676 Min Nonbonded Distance : 2.233 Molprobity Statistics. All-atom Clashscore : 4.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.96 % Favored : 93.04 % Rotamer: Outliers : 2.20 % Allowed : 22.40 % Favored : 75.40 % 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: 0.51 (0.36), residues: 589 helix: 1.85 (0.28), residues: 345 sheet: -1.94 (0.65), residues: 57 loop : -1.83 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.000 HIS A 291 PHE 0.016 0.001 PHE A 48 TYR 0.012 0.001 TYR A 634 ARG 0.006 0.000 ARG A 266 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8502 (OUTLIER) cc_final: 0.8153 (mmm) REVERT: A 404 MET cc_start: 0.4735 (OUTLIER) cc_final: 0.3383 (pmm) REVERT: B 112 GLU cc_start: 0.7777 (OUTLIER) cc_final: 0.7285 (pm20) outliers start: 11 outliers final: 8 residues processed: 70 average time/residue: 0.3492 time to fit residues: 31.9793 Evaluate side-chains 74 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 63 time to evaluate : 0.727 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 19 optimal weight: 0.9990 chunk 7 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3839 r_free = 0.3839 target = 0.164163 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3515 r_free = 0.3515 target = 0.137015 restraints weight = 15014.227| |-----------------------------------------------------------------------------| r_work (start): 0.3491 rms_B_bonded: 1.61 r_work: 0.3344 rms_B_bonded: 2.31 restraints_weight: 0.5000 r_work: 0.3224 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8349 moved from start: 0.1445 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4842 Z= 0.213 Angle : 0.538 4.975 6583 Z= 0.283 Chirality : 0.038 0.150 738 Planarity : 0.004 0.045 814 Dihedral : 11.218 135.378 676 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 2.60 % Allowed : 21.80 % Favored : 75.60 % 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: 0.45 (0.36), residues: 589 helix: 1.79 (0.28), residues: 345 sheet: -2.04 (0.63), residues: 57 loop : -1.83 (0.44), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 107 HIS 0.002 0.001 HIS A 291 PHE 0.017 0.001 PHE A 48 TYR 0.013 0.001 TYR A 634 ARG 0.006 0.000 ARG A 266 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1178 Ramachandran restraints generated. 589 Oldfield, 0 Emsley, 589 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.701 Fit side-chains revert: symmetry clash REVERT: A 311 MET cc_start: 0.8472 (OUTLIER) cc_final: 0.8110 (mmm) REVERT: A 404 MET cc_start: 0.4789 (OUTLIER) cc_final: 0.3478 (pmm) REVERT: B 112 GLU cc_start: 0.7774 (OUTLIER) cc_final: 0.7268 (pm20) outliers start: 13 outliers final: 10 residues processed: 72 average time/residue: 0.3357 time to fit residues: 31.9450 Evaluate side-chains 77 residues out of total 500 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.708 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 SER Chi-restraints excluded: chain A residue 48 PHE Chi-restraints excluded: chain A residue 52 ASN Chi-restraints excluded: chain A residue 212 PHE Chi-restraints excluded: chain A residue 214 GLN Chi-restraints excluded: chain A residue 311 MET Chi-restraints excluded: chain A residue 316 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 404 MET Chi-restraints excluded: chain A residue 663 VAL Chi-restraints excluded: chain B residue 104 THR Chi-restraints excluded: chain B residue 112 GLU Chi-restraints excluded: chain B residue 124 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 59 random chunks: chunk 35 optimal weight: 0.9990 chunk 8 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 54 optimal weight: 0.9990 chunk 9 optimal weight: 0.4980 chunk 48 optimal weight: 0.0970 chunk 22 optimal weight: 0.2980 chunk 46 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 38 optimal weight: 0.0770 chunk 34 optimal weight: 0.1980 overall best weight: 0.2336 ------------------------------------------------------------------------------- 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 = 0.3876 r_free = 0.3876 target = 0.167556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.140659 restraints weight = 14908.850| |-----------------------------------------------------------------------------| r_work (start): 0.3542 rms_B_bonded: 1.62 r_work: 0.3375 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3255 rms_B_bonded: 4.10 restraints_weight: 0.2500 r_work (final): 0.3255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8317 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4842 Z= 0.138 Angle : 0.506 4.654 6583 Z= 0.265 Chirality : 0.037 0.146 738 Planarity : 0.004 0.043 814 Dihedral : 11.107 133.254 676 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 4.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer: Outliers : 2.20 % Allowed : 22.20 % Favored : 75.60 % 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: 0.72 (0.36), residues: 589 helix: 2.07 (0.29), residues: 345 sheet: -1.99 (0.65), residues: 57 loop : -1.82 (0.43), residues: 187 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 280 HIS 0.001 0.000 HIS A 291 PHE 0.011 0.001 PHE A 48 TYR 0.010 0.001 TYR A 183 ARG 0.005 0.000 ARG A 266 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5624.01 seconds wall clock time: 100 minutes 7.26 seconds (6007.26 seconds total)