Starting phenix.real_space_refine on Tue Feb 11 03:44:24 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wn1_32619/02_2025/7wn1_32619.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wn1_32619/02_2025/7wn1_32619.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.11 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wn1_32619/02_2025/7wn1_32619.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wn1_32619/02_2025/7wn1_32619.map" model { file = "/net/cci-nas-00/data/ceres_data/7wn1_32619/02_2025/7wn1_32619.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wn1_32619/02_2025/7wn1_32619.cif" } resolution = 3.11 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= 0.033 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 26 5.16 5 C 2572 2.51 5 N 616 2.21 5 O 687 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3901 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2953 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 1 Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'NOS%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 3.37, per 1000 atoms: 0.86 Number of scatterers: 3901 At special positions: 0 Unit cell: (110.39, 60.59, 64.74, 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 26 16.00 O 687 8.00 N 616 7.00 C 2572 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " 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: 1.11 Conformation dependent library (CDL) restraints added in 464.2 milliseconds 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 914 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 3 sheets defined 64.3% alpha, 13.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'A' and resid 31 through 59 removed outlier: 4.331A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.778A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.547A pdb=" N ASN A 66 " --> pdb=" O ASN A 62 " (cutoff:3.500A) removed outlier: 4.022A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 111 Processing helix chain 'A' and resid 112 through 144 Processing helix chain 'A' and resid 149 through 175 removed outlier: 3.802A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N PHE A 174 " --> pdb=" O LEU A 170 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 210 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 239 through 257 removed outlier: 3.734A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ASN A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 removed outlier: 3.674A pdb=" N GLN A 266 " --> pdb=" O HIS A 262 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N GLU A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.759A pdb=" N THR A 277 " --> pdb=" O ASP A 273 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N PHE A 283 " --> pdb=" O ILE A 279 " (cutoff:3.500A) removed outlier: 3.660A pdb=" N PHE A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 removed outlier: 3.967A pdb=" N ASN A 295 " --> pdb=" O ARG A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 319 Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.538A pdb=" N TRP A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA A 330 " --> pdb=" O PHE A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 369 removed outlier: 3.804A pdb=" N LEU A 350 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N THR A 359 " --> pdb=" O GLY A 355 " (cutoff:3.500A) Proline residue: A 361 - end of helix removed outlier: 5.181A pdb=" N VAL A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N LYS A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 400 removed outlier: 3.655A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 3.684A pdb=" N THR A 400 " --> pdb=" O GLY A 396 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 405 Processing helix chain 'C' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'C' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 5.513A pdb=" N ARG C 38 " --> pdb=" O LEU C 47 " (cutoff:3.500A) removed outlier: 5.386A pdb=" N LEU C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.193A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N GLN C 109 " --> pdb=" O THR C 99 " (cutoff:3.500A) 260 hydrogen bonds defined for protein. 750 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: 1.13 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 823 1.33 - 1.45: 929 1.45 - 1.57: 2205 1.57 - 1.69: 2 1.69 - 1.81: 39 Bond restraints: 3998 Sorted by residual: bond pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.415 1.600 -0.185 1.50e-02 4.44e+03 1.53e+02 bond pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " ideal model delta sigma weight residual 1.526 1.346 0.180 1.50e-02 4.44e+03 1.44e+02 bond pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.454 1.309 0.145 1.50e-02 4.44e+03 9.32e+01 bond pdb=" C2 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.293 1.444 -0.151 2.00e-02 2.50e+03 5.67e+01 bond pdb=" C4 NOS A 501 " pdb=" N3 NOS A 501 " ideal model delta sigma weight residual 1.347 1.497 -0.150 2.00e-02 2.50e+03 5.66e+01 ... (remaining 3993 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.00: 5332 2.00 - 4.00: 75 4.00 - 6.00: 16 6.00 - 8.00: 5 8.00 - 10.00: 1 Bond angle restraints: 5429 Sorted by residual: angle pdb=" C3' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" O2' NOS A 501 " ideal model delta sigma weight residual 114.60 107.68 6.92 1.50e+00 4.44e-01 2.13e+01 angle pdb=" C3' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" C5' NOS A 501 " ideal model delta sigma weight residual 115.20 109.44 5.76 1.50e+00 4.44e-01 1.47e+01 angle pdb=" C1' NOS A 501 " pdb=" O4' NOS A 501 " pdb=" C4' NOS A 501 " ideal model delta sigma weight residual 109.70 106.15 3.55 1.00e+00 1.00e+00 1.26e+01 angle pdb=" C2' NOS A 501 " pdb=" C1' NOS A 501 " pdb=" N9 NOS A 501 " ideal model delta sigma weight residual 114.00 108.75 5.25 1.50e+00 4.44e-01 1.23e+01 angle pdb=" C1' NOS A 501 " pdb=" C2' NOS A 501 " pdb=" C3' NOS A 501 " ideal model delta sigma weight residual 101.50 104.96 -3.46 1.00e+00 1.00e+00 1.20e+01 ... (remaining 5424 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.24: 2049 15.24 - 30.48: 201 30.48 - 45.71: 53 45.71 - 60.95: 17 60.95 - 76.19: 3 Dihedral angle restraints: 2323 sinusoidal: 899 harmonic: 1424 Sorted by residual: dihedral pdb=" C2' NOS A 501 " pdb=" C3' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sinusoidal sigma weight residual 24.00 -2.88 26.88 1 8.00e+00 1.56e-02 1.62e+01 dihedral pdb=" C1' NOS A 501 " pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " pdb=" C3' NOS A 501 " ideal model delta sinusoidal sigma weight residual 2.00 -22.80 24.80 1 8.00e+00 1.56e-02 1.38e+01 dihedral pdb=" CA LEU A 256 " pdb=" C LEU A 256 " pdb=" N PHE A 257 " pdb=" CA PHE A 257 " ideal model delta harmonic sigma weight residual -180.00 -161.88 -18.12 0 5.00e+00 4.00e-02 1.31e+01 ... (remaining 2320 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 372 0.031 - 0.061: 173 0.061 - 0.092: 57 0.092 - 0.122: 20 0.122 - 0.153: 8 Chirality restraints: 630 Sorted by residual: chirality pdb=" CB ILE A 193 " pdb=" CA ILE A 193 " pdb=" CG1 ILE A 193 " pdb=" CG2 ILE A 193 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.82e-01 chirality pdb=" CA ASP A 147 " pdb=" N ASP A 147 " pdb=" C ASP A 147 " pdb=" CB ASP A 147 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA PHE A 307 " pdb=" N PHE A 307 " pdb=" C PHE A 307 " pdb=" CB PHE A 307 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.59e-01 ... (remaining 627 not shown) Planarity restraints: 665 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 257 " -0.023 5.00e-02 4.00e+02 3.53e-02 1.99e+00 pdb=" N PRO A 258 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS A 334 " -0.021 5.00e-02 4.00e+02 3.24e-02 1.68e+00 pdb=" N PRO A 335 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO A 335 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 335 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 412 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 413 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 413 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 413 " -0.017 5.00e-02 4.00e+02 ... (remaining 662 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 835 2.78 - 3.31: 3841 3.31 - 3.84: 6568 3.84 - 4.37: 7875 4.37 - 4.90: 13686 Nonbonded interactions: 32805 Sorted by model distance: nonbonded pdb=" OH TYR A 65 " pdb=" OD1 ASP A 117 " model vdw 2.246 3.040 nonbonded pdb=" OG1 THR A 41 " pdb=" OD1 ASN A 209 " model vdw 2.256 3.040 nonbonded pdb=" O CYS A 395 " pdb=" OG1 THR A 399 " model vdw 2.283 3.040 nonbonded pdb=" O LEU A 256 " pdb=" N GLY A 261 " model vdw 2.320 3.120 nonbonded pdb=" NE2 GLN C 81 " pdb=" OD1 ASN C 83 " model vdw 2.320 3.120 ... (remaining 32800 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: 1.020 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: 0.160 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 14.340 Find NCS groups from input model: 0.040 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:2.950 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.580 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8367 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 : 0.007 0.185 3998 Z= 0.429 Angle : 0.648 10.003 5429 Z= 0.352 Chirality : 0.042 0.153 630 Planarity : 0.004 0.035 665 Dihedral : 13.827 76.187 1406 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % 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: 1.00 (0.38), residues: 487 helix: 1.09 (0.30), residues: 285 sheet: 0.84 (0.64), residues: 58 loop : -0.10 (0.58), residues: 144 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 251 HIS 0.004 0.001 HIS A 334 PHE 0.016 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.444 Fit side-chains REVERT: A 175 VAL cc_start: 0.8097 (t) cc_final: 0.7828 (m) REVERT: A 303 LYS cc_start: 0.8628 (tppt) cc_final: 0.8418 (tppt) REVERT: A 407 ASN cc_start: 0.8197 (t0) cc_final: 0.7963 (t0) REVERT: C 94 TYR cc_start: 0.8213 (m-10) cc_final: 0.8003 (m-10) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.1524 time to fit residues: 14.0749 Evaluate side-chains 62 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 4.9990 chunk 37 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 9.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.5980 chunk 28 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 209 ASN C 58 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.113378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.100168 restraints weight = 5145.663| |-----------------------------------------------------------------------------| r_work (start): 0.3147 rms_B_bonded: 1.61 r_work: 0.3057 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.2943 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.1085 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3998 Z= 0.220 Angle : 0.574 6.538 5429 Z= 0.310 Chirality : 0.043 0.144 630 Planarity : 0.004 0.033 665 Dihedral : 5.598 37.655 540 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.33 % Allowed : 5.58 % Favored : 92.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.39 (0.38), residues: 487 helix: 1.49 (0.29), residues: 289 sheet: 0.96 (0.64), residues: 58 loop : -0.17 (0.57), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.004 0.001 HIS A 180 PHE 0.017 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.002 0.001 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 63 time to evaluate : 0.415 Fit side-chains REVERT: A 303 LYS cc_start: 0.8776 (tppt) cc_final: 0.8560 (tppt) REVERT: A 407 ASN cc_start: 0.8462 (t0) cc_final: 0.8103 (t0) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.1556 time to fit residues: 13.0409 Evaluate side-chains 61 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 55 time to evaluate : 0.466 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 233 MET Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 39 GLN Chi-restraints excluded: chain C residue 82 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 46 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 overall best weight: 0.7678 ------------------------------------------------------------------------------- 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 = 0.3340 r_free = 0.3340 target = 0.112630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.099557 restraints weight = 5107.325| |-----------------------------------------------------------------------------| r_work (start): 0.3142 rms_B_bonded: 1.57 r_work: 0.3054 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.2940 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.2940 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8585 moved from start: 0.1325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3998 Z= 0.217 Angle : 0.543 6.488 5429 Z= 0.293 Chirality : 0.043 0.144 630 Planarity : 0.004 0.034 665 Dihedral : 5.218 32.631 540 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.33 % Allowed : 9.53 % Favored : 88.14 % 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: 1.68 (0.38), residues: 487 helix: 1.70 (0.29), residues: 289 sheet: 1.09 (0.64), residues: 58 loop : -0.01 (0.59), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.016 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 303 LYS cc_start: 0.8785 (tppt) cc_final: 0.8562 (tppt) REVERT: A 407 ASN cc_start: 0.8423 (t0) cc_final: 0.8073 (t0) outliers start: 10 outliers final: 8 residues processed: 63 average time/residue: 0.1550 time to fit residues: 12.6225 Evaluate side-chains 65 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 273 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.8980 chunk 30 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 28 optimal weight: 0.0980 chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 0.0870 chunk 39 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 40 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3373 r_free = 0.3373 target = 0.115017 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.101391 restraints weight = 5095.741| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 1.62 r_work: 0.3092 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.2978 rms_B_bonded: 3.34 restraints_weight: 0.2500 r_work (final): 0.2978 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8549 moved from start: 0.1577 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3998 Z= 0.171 Angle : 0.516 6.577 5429 Z= 0.276 Chirality : 0.042 0.146 630 Planarity : 0.004 0.034 665 Dihedral : 4.957 28.424 540 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 2.79 % Allowed : 13.02 % Favored : 84.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.38), residues: 487 helix: 1.94 (0.29), residues: 288 sheet: 1.12 (0.64), residues: 58 loop : 0.03 (0.59), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.014 0.001 PHE C 27 TYR 0.019 0.001 TYR C 102 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.421 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8490 (OUTLIER) cc_final: 0.8253 (m-30) REVERT: A 303 LYS cc_start: 0.8784 (tppt) cc_final: 0.8555 (tppt) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.1539 time to fit residues: 12.9944 Evaluate side-chains 68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 59 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 28 optimal weight: 0.4980 chunk 25 optimal weight: 0.6980 chunk 31 optimal weight: 0.0060 chunk 19 optimal weight: 0.4980 chunk 43 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 16 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 46 optimal weight: 4.9990 chunk 21 optimal weight: 0.8980 overall best weight: 0.4596 ------------------------------------------------------------------------------- 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 = 0.3413 r_free = 0.3413 target = 0.117484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103728 restraints weight = 5184.090| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 1.61 r_work: 0.3136 rms_B_bonded: 1.92 restraints_weight: 0.5000 r_work: 0.3021 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.1684 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3998 Z= 0.167 Angle : 0.509 6.468 5429 Z= 0.273 Chirality : 0.041 0.150 630 Planarity : 0.004 0.035 665 Dihedral : 4.800 26.948 540 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.56 % Allowed : 14.42 % Favored : 83.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.38), residues: 487 helix: 1.92 (0.29), residues: 293 sheet: 1.15 (0.64), residues: 58 loop : 0.13 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.014 0.001 PHE C 27 TYR 0.015 0.001 TYR C 102 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.398 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8297 (m-30) outliers start: 11 outliers final: 6 residues processed: 65 average time/residue: 0.1451 time to fit residues: 12.1564 Evaluate side-chains 62 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.410 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 43 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 38 optimal weight: 0.0000 chunk 41 optimal weight: 0.0470 chunk 35 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 9 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 overall best weight: 0.4882 ------------------------------------------------------------------------------- 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 = 0.3394 r_free = 0.3394 target = 0.115805 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.102220 restraints weight = 5115.002| |-----------------------------------------------------------------------------| r_work (start): 0.3203 rms_B_bonded: 1.58 r_work: 0.3120 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3008 rms_B_bonded: 3.31 restraints_weight: 0.2500 r_work (final): 0.3008 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8554 moved from start: 0.1831 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3998 Z= 0.169 Angle : 0.515 7.672 5429 Z= 0.272 Chirality : 0.041 0.153 630 Planarity : 0.004 0.035 665 Dihedral : 4.686 27.213 540 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 2.79 % Allowed : 14.65 % Favored : 82.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.11 (0.38), residues: 487 helix: 2.02 (0.29), residues: 293 sheet: 1.26 (0.65), residues: 58 loop : 0.18 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.013 0.001 PHE C 27 TYR 0.015 0.001 TYR C 102 ARG 0.001 0.000 ARG A 291 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: A 113 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: A 407 ASN cc_start: 0.8412 (t0) cc_final: 0.8038 (t0) outliers start: 12 outliers final: 10 residues processed: 61 average time/residue: 0.1465 time to fit residues: 11.6033 Evaluate side-chains 63 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 52 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 0.0170 chunk 10 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 12 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 40 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- 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 = 0.3409 r_free = 0.3409 target = 0.117145 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.103372 restraints weight = 5041.065| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 1.60 r_work: 0.3130 rms_B_bonded: 1.91 restraints_weight: 0.5000 r_work: 0.3017 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8572 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3998 Z= 0.182 Angle : 0.514 6.704 5429 Z= 0.274 Chirality : 0.042 0.152 630 Planarity : 0.004 0.035 665 Dihedral : 4.651 27.276 540 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.49 % Allowed : 14.65 % Favored : 81.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.12 (0.38), residues: 487 helix: 2.02 (0.29), residues: 293 sheet: 1.30 (0.66), residues: 58 loop : 0.19 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.002 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 56 time to evaluate : 0.419 Fit side-chains REVERT: A 113 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8280 (m-30) REVERT: A 407 ASN cc_start: 0.8404 (t0) cc_final: 0.8046 (t0) outliers start: 15 outliers final: 11 residues processed: 64 average time/residue: 0.1473 time to fit residues: 12.2784 Evaluate side-chains 68 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 6 GLU Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 5 optimal weight: 0.1980 chunk 12 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 45 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 28 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 0.4538 ------------------------------------------------------------------------------- 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 = 0.3408 r_free = 0.3408 target = 0.116728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.103292 restraints weight = 5076.740| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 1.59 r_work: 0.3134 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3022 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3022 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3998 Z= 0.168 Angle : 0.509 6.663 5429 Z= 0.271 Chirality : 0.041 0.155 630 Planarity : 0.004 0.035 665 Dihedral : 4.580 27.776 540 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 7.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.31 % Favored : 95.69 % Rotamer: Outliers : 3.95 % Allowed : 14.65 % Favored : 81.40 % 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: 2.22 (0.38), residues: 487 helix: 2.09 (0.29), residues: 293 sheet: 1.35 (0.66), residues: 58 loop : 0.23 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 251 HIS 0.002 0.001 HIS A 334 PHE 0.012 0.001 PHE C 27 TYR 0.015 0.001 TYR C 102 ARG 0.001 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 60 time to evaluate : 0.461 Fit side-chains REVERT: A 113 ASP cc_start: 0.8505 (OUTLIER) cc_final: 0.8266 (m-30) REVERT: A 407 ASN cc_start: 0.8398 (t0) cc_final: 0.8036 (t0) REVERT: C 64 LYS cc_start: 0.7466 (tppt) cc_final: 0.7170 (mttp) outliers start: 17 outliers final: 11 residues processed: 70 average time/residue: 0.1443 time to fit residues: 13.0727 Evaluate side-chains 66 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 32 optimal weight: 0.0870 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 36 optimal weight: 0.8980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- 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 = 0.3393 r_free = 0.3393 target = 0.115860 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.102146 restraints weight = 5065.131| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 1.60 r_work: 0.3123 rms_B_bonded: 1.89 restraints_weight: 0.5000 r_work: 0.3015 rms_B_bonded: 3.29 restraints_weight: 0.2500 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8583 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3998 Z= 0.191 Angle : 0.518 6.360 5429 Z= 0.276 Chirality : 0.041 0.161 630 Planarity : 0.004 0.035 665 Dihedral : 4.585 27.080 540 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.49 % Allowed : 15.35 % Favored : 81.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.16 (0.38), residues: 487 helix: 2.04 (0.29), residues: 293 sheet: 1.25 (0.67), residues: 58 loop : 0.24 (0.60), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.016 0.001 TYR C 102 ARG 0.002 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.454 Fit side-chains REVERT: A 113 ASP cc_start: 0.8507 (OUTLIER) cc_final: 0.8271 (m-30) REVERT: A 187 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8442 (tttm) REVERT: A 407 ASN cc_start: 0.8383 (t0) cc_final: 0.8048 (t0) REVERT: C 64 LYS cc_start: 0.7530 (tppt) cc_final: 0.7222 (mttp) outliers start: 15 outliers final: 13 residues processed: 67 average time/residue: 0.1400 time to fit residues: 12.2360 Evaluate side-chains 72 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 57 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 148 ASN Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 203 ILE Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 13 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8384 ------------------------------------------------------------------------------- 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 = 0.3366 r_free = 0.3366 target = 0.113925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.100168 restraints weight = 5130.875| |-----------------------------------------------------------------------------| r_work (start): 0.3154 rms_B_bonded: 1.59 r_work: 0.3069 rms_B_bonded: 1.90 restraints_weight: 0.5000 r_work: 0.2954 rms_B_bonded: 3.33 restraints_weight: 0.2500 r_work (final): 0.2954 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8593 moved from start: 0.1964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3998 Z= 0.223 Angle : 0.542 7.553 5429 Z= 0.290 Chirality : 0.042 0.163 630 Planarity : 0.004 0.035 665 Dihedral : 4.676 26.503 540 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.02 % Allowed : 15.58 % Favored : 81.40 % 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: 2.04 (0.38), residues: 487 helix: 1.98 (0.29), residues: 294 sheet: 1.14 (0.65), residues: 59 loop : 0.14 (0.60), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.002 0.000 ARG C 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 974 Ramachandran restraints generated. 487 Oldfield, 0 Emsley, 487 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.380 Fit side-chains REVERT: A 113 ASP cc_start: 0.8491 (OUTLIER) cc_final: 0.8262 (m-30) REVERT: A 187 LYS cc_start: 0.8716 (OUTLIER) cc_final: 0.8466 (tttm) REVERT: A 375 LYS cc_start: 0.8493 (ttmm) cc_final: 0.8163 (mmtm) REVERT: A 407 ASN cc_start: 0.8383 (t0) cc_final: 0.8047 (t0) REVERT: C 64 LYS cc_start: 0.7516 (tppt) cc_final: 0.7186 (mttp) outliers start: 13 outliers final: 11 residues processed: 65 average time/residue: 0.1427 time to fit residues: 11.9317 Evaluate side-chains 70 residues out of total 430 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 57 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 61 ILE Chi-restraints excluded: chain A residue 113 ASP Chi-restraints excluded: chain A residue 143 SER Chi-restraints excluded: chain A residue 168 ASN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 297 THR Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 334 HIS Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 43 LYS Chi-restraints excluded: chain C residue 82 MET Chi-restraints excluded: chain C residue 88 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 5.9990 chunk 3 optimal weight: 0.9990 chunk 38 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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 = 0.3343 r_free = 0.3343 target = 0.112662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.098604 restraints weight = 5032.818| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 1.65 r_work: 0.3047 rms_B_bonded: 1.94 restraints_weight: 0.5000 r_work: 0.2933 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2933 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8575 moved from start: 0.1978 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3998 Z= 0.212 Angle : 0.535 7.239 5429 Z= 0.286 Chirality : 0.042 0.162 630 Planarity : 0.004 0.035 665 Dihedral : 4.685 26.045 540 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % Rotamer: Outliers : 3.02 % Allowed : 15.35 % Favored : 81.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.04 (0.38), residues: 487 helix: 1.98 (0.29), residues: 294 sheet: 1.15 (0.65), residues: 59 loop : 0.11 (0.59), residues: 134 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 251 HIS 0.002 0.001 HIS A 180 PHE 0.013 0.001 PHE C 27 TYR 0.018 0.001 TYR C 102 ARG 0.002 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2074.45 seconds wall clock time: 37 minutes 34.03 seconds (2254.03 seconds total)