Starting phenix.real_space_refine on Wed Mar 5 17:40:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jrl_61759/03_2025/9jrl_61759_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jrl_61759/03_2025/9jrl_61759.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.25 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jrl_61759/03_2025/9jrl_61759.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jrl_61759/03_2025/9jrl_61759.map" model { file = "/net/cci-nas-00/data/ceres_data/9jrl_61759/03_2025/9jrl_61759_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jrl_61759/03_2025/9jrl_61759_neut.cif" } resolution = 3.25 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= 0.086 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 10 5.16 5 C 2103 2.51 5 N 517 2.21 5 O 515 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3145 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3103 Number of conformers: 1 Conformer: "" Number of residues, atoms: 386, 3103 Classifications: {'peptide': 386} Link IDs: {'PTRANS': 12, 'TRANS': 373} Chain breaks: 2 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 42 Unusual residues: {'COP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.88, per 1000 atoms: 0.92 Number of scatterers: 3145 At special positions: 0 Unit cell: (68, 65, 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 10 16.00 O 515 8.00 N 517 7.00 C 2103 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.92 Conformation dependent library (CDL) restraints added in 373.3 milliseconds 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 730 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 90.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 25 through 40 removed outlier: 4.687A pdb=" N VAL A 29 " --> pdb=" O TRP A 25 " (cutoff:3.500A) removed outlier: 3.700A pdb=" N GLN A 40 " --> pdb=" O GLY A 36 " (cutoff:3.500A) Processing helix chain 'A' and resid 41 through 46 removed outlier: 6.884A pdb=" N GLY A 44 " --> pdb=" O ILE A 41 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N SER A 46 " --> pdb=" O PRO A 43 " (cutoff:3.500A) Processing helix chain 'A' and resid 47 through 54 Processing helix chain 'A' and resid 60 through 68 removed outlier: 3.642A pdb=" N ILE A 68 " --> pdb=" O VAL A 64 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 87 removed outlier: 4.518A pdb=" N VAL A 81 " --> pdb=" O LEU A 77 " (cutoff:3.500A) Proline residue: A 82 - end of helix Processing helix chain 'A' and resid 91 through 112 removed outlier: 4.164A pdb=" N VAL A 95 " --> pdb=" O ARG A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 131 removed outlier: 3.521A pdb=" N MET A 119 " --> pdb=" O SER A 115 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 143 removed outlier: 3.646A pdb=" N TYR A 136 " --> pdb=" O ALA A 132 " (cutoff:3.500A) Processing helix chain 'A' and resid 145 through 147 No H-bonds generated for 'chain 'A' and resid 145 through 147' Processing helix chain 'A' and resid 148 through 177 removed outlier: 3.590A pdb=" N ARG A 157 " --> pdb=" O ALA A 153 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 202 removed outlier: 3.802A pdb=" N PHE A 202 " --> pdb=" O VAL A 198 " (cutoff:3.500A) Processing helix chain 'A' and resid 250 through 263 Processing helix chain 'A' and resid 264 through 295 removed outlier: 3.914A pdb=" N ALA A 279 " --> pdb=" O VAL A 275 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N GLY A 280 " --> pdb=" O PHE A 276 " (cutoff:3.500A) removed outlier: 4.169A pdb=" N HIS A 289 " --> pdb=" O VAL A 285 " (cutoff:3.500A) removed outlier: 4.544A pdb=" N ILE A 290 " --> pdb=" O TYR A 286 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N VAL A 295 " --> pdb=" O LEU A 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 327 removed outlier: 3.621A pdb=" N PHE A 326 " --> pdb=" O PHE A 322 " (cutoff:3.500A) Processing helix chain 'A' and resid 335 through 356 Processing helix chain 'A' and resid 358 through 360 No H-bonds generated for 'chain 'A' and resid 358 through 360' Processing helix chain 'A' and resid 361 through 390 removed outlier: 3.578A pdb=" N CYS A 365 " --> pdb=" O SER A 361 " (cutoff:3.500A) Proline residue: A 381 - end of helix removed outlier: 3.515A pdb=" N SER A 390 " --> pdb=" O GLN A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 394 removed outlier: 7.400A pdb=" N GLU A 394 " --> pdb=" O LEU A 391 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 391 through 394' Processing helix chain 'A' and resid 395 through 418 Processing helix chain 'A' and resid 427 through 456 246 hydrogen bonds defined for protein. 735 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 1.03 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: 584 1.33 - 1.45: 878 1.45 - 1.57: 1756 1.57 - 1.69: 0 1.69 - 1.81: 16 Bond restraints: 3234 Sorted by residual: bond pdb=" C39 COP A 701 " pdb=" O41 COP A 701 " ideal model delta sigma weight residual 1.246 1.332 -0.086 2.00e-02 2.50e+03 1.86e+01 bond pdb=" N THR A 49 " pdb=" CA THR A 49 " ideal model delta sigma weight residual 1.462 1.487 -0.025 7.70e-03 1.69e+04 1.08e+01 bond pdb=" N VAL A 418 " pdb=" CA VAL A 418 " ideal model delta sigma weight residual 1.459 1.498 -0.039 1.25e-02 6.40e+03 9.96e+00 bond pdb=" N VAL A 144 " pdb=" CA VAL A 144 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.14e-02 7.69e+03 9.19e+00 bond pdb=" C1 COP A 701 " pdb=" C10 COP A 701 " ideal model delta sigma weight residual 1.443 1.384 0.059 2.00e-02 2.50e+03 8.60e+00 ... (remaining 3229 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.57: 4215 1.57 - 3.14: 160 3.14 - 4.71: 21 4.71 - 6.27: 5 6.27 - 7.84: 5 Bond angle restraints: 4406 Sorted by residual: angle pdb=" CA HIS A 289 " pdb=" CB HIS A 289 " pdb=" CG HIS A 289 " ideal model delta sigma weight residual 113.80 107.01 6.79 1.00e+00 1.00e+00 4.61e+01 angle pdb=" CB HIS A 289 " pdb=" CG HIS A 289 " pdb=" CD2 HIS A 289 " ideal model delta sigma weight residual 131.20 125.70 5.50 1.30e+00 5.92e-01 1.79e+01 angle pdb=" CB HIS A 289 " pdb=" CG HIS A 289 " pdb=" ND1 HIS A 289 " ideal model delta sigma weight residual 122.70 127.38 -4.68 1.50e+00 4.44e-01 9.75e+00 angle pdb=" CA VAL A 152 " pdb=" C VAL A 152 " pdb=" O VAL A 152 " ideal model delta sigma weight residual 120.95 117.98 2.97 1.04e+00 9.25e-01 8.13e+00 angle pdb=" N PHE A 103 " pdb=" CA PHE A 103 " pdb=" C PHE A 103 " ideal model delta sigma weight residual 111.36 108.34 3.02 1.09e+00 8.42e-01 7.68e+00 ... (remaining 4401 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.74: 1536 16.74 - 33.48: 226 33.48 - 50.22: 68 50.22 - 66.96: 9 66.96 - 83.70: 4 Dihedral angle restraints: 1843 sinusoidal: 707 harmonic: 1136 Sorted by residual: dihedral pdb=" CA ARG A 26 " pdb=" C ARG A 26 " pdb=" N HIS A 27 " pdb=" CA HIS A 27 " ideal model delta harmonic sigma weight residual -180.00 -163.04 -16.96 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CA LEU A 395 " pdb=" C LEU A 395 " pdb=" N CYS A 396 " pdb=" CA CYS A 396 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 dihedral pdb=" CA SER A 419 " pdb=" C SER A 419 " pdb=" N ASP A 420 " pdb=" CA ASP A 420 " ideal model delta harmonic sigma weight residual 180.00 -163.80 -16.20 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1840 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 374 0.042 - 0.085: 107 0.085 - 0.127: 24 0.127 - 0.169: 3 0.169 - 0.212: 2 Chirality restraints: 510 Sorted by residual: chirality pdb=" CA LEU A 337 " pdb=" N LEU A 337 " pdb=" C LEU A 337 " pdb=" CB LEU A 337 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.12e+00 chirality pdb=" CB VAL A 418 " pdb=" CA VAL A 418 " pdb=" CG1 VAL A 418 " pdb=" CG2 VAL A 418 " both_signs ideal model delta sigma weight residual False -2.63 -2.43 -0.19 2.00e-01 2.50e+01 9.43e-01 chirality pdb=" CA VAL A 152 " pdb=" N VAL A 152 " pdb=" C VAL A 152 " pdb=" CB VAL A 152 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.04e-01 ... (remaining 507 not shown) Planarity restraints: 526 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C29 COP A 701 " -0.333 2.00e-02 2.50e+03 2.82e-01 9.91e+02 pdb=" C31 COP A 701 " 0.086 2.00e-02 2.50e+03 pdb=" C33 COP A 701 " -0.184 2.00e-02 2.50e+03 pdb=" N30 COP A 701 " 0.491 2.00e-02 2.50e+03 pdb=" O32 COP A 701 " -0.060 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C16 COP A 701 " 0.113 2.00e-02 2.50e+03 1.31e-01 2.13e+02 pdb=" C19 COP A 701 " -0.033 2.00e-02 2.50e+03 pdb=" C21 COP A 701 " 0.156 2.00e-02 2.50e+03 pdb=" N20 COP A 701 " -0.216 2.00e-02 2.50e+03 pdb=" O19 COP A 701 " -0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 168 " 0.010 2.00e-02 2.50e+03 1.91e-02 3.65e+00 pdb=" C SER A 168 " -0.033 2.00e-02 2.50e+03 pdb=" O SER A 168 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 169 " 0.011 2.00e-02 2.50e+03 ... (remaining 523 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 768 2.78 - 3.31: 3190 3.31 - 3.84: 5601 3.84 - 4.37: 6300 4.37 - 4.90: 10802 Nonbonded interactions: 26661 Sorted by model distance: nonbonded pdb=" O PHE A 276 " pdb=" OH TYR A 438 " model vdw 2.251 3.040 nonbonded pdb=" OH TYR A 31 " pdb=" O LEU A 199 " model vdw 2.261 3.040 nonbonded pdb=" OH TYR A 139 " pdb=" O LYS A 204 " model vdw 2.271 3.040 nonbonded pdb=" OE1 GLU A 45 " pdb=" OH TYR A 126 " model vdw 2.301 3.040 nonbonded pdb=" NH2 ARG A 157 " pdb=" OE1 GLN A 377 " model vdw 2.302 3.120 ... (remaining 26656 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.420 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.330 Find NCS groups from input model: 0.030 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:2.970 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 : 0.005 0.086 3234 Z= 0.307 Angle : 0.693 7.843 4406 Z= 0.408 Chirality : 0.042 0.212 510 Planarity : 0.015 0.282 526 Dihedral : 17.250 83.705 1113 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.51 % Allowed : 23.49 % Favored : 75.00 % 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: 0.55 (0.42), residues: 380 helix: 0.86 (0.28), residues: 318 sheet: None (None), residues: 0 loop : -1.92 (0.72), residues: 62 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 270 HIS 0.007 0.001 HIS A 289 PHE 0.025 0.001 PHE A 84 TYR 0.011 0.001 TYR A 31 ARG 0.001 0.000 ARG A 330 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 28 time to evaluate : 0.338 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 32 average time/residue: 0.2464 time to fit residues: 9.3532 Evaluate side-chains 27 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 26 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 GLU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 0.6980 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 29 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142225 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.117743 restraints weight = 3568.313| |-----------------------------------------------------------------------------| r_work (start): 0.3277 rms_B_bonded: 1.74 r_work: 0.3146 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3003 rms_B_bonded: 4.12 restraints_weight: 0.2500 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7603 moved from start: 0.0839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3234 Z= 0.281 Angle : 0.580 6.246 4406 Z= 0.294 Chirality : 0.039 0.146 510 Planarity : 0.005 0.050 526 Dihedral : 7.565 74.095 449 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 3.92 % Allowed : 22.89 % Favored : 73.19 % 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 (0.43), residues: 380 helix: 1.83 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.85 (0.79), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 107 HIS 0.002 0.001 HIS A 358 PHE 0.025 0.002 PHE A 84 TYR 0.013 0.001 TYR A 438 ARG 0.002 0.000 ARG A 151 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 30 time to evaluate : 0.340 Fit side-chains REVERT: A 32 LEU cc_start: 0.7948 (OUTLIER) cc_final: 0.7641 (tp) REVERT: A 155 TYR cc_start: 0.8572 (m-10) cc_final: 0.8239 (m-10) REVERT: A 289 HIS cc_start: 0.7911 (m-70) cc_final: 0.7651 (m-70) REVERT: A 424 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6631 (tt) outliers start: 13 outliers final: 7 residues processed: 40 average time/residue: 0.1701 time to fit residues: 8.3953 Evaluate side-chains 37 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 28 time to evaluate : 0.342 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 32 LEU Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.6980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 1 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.142208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.116907 restraints weight = 3624.653| |-----------------------------------------------------------------------------| r_work (start): 0.3256 rms_B_bonded: 1.82 r_work: 0.3130 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2985 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.1077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3234 Z= 0.262 Angle : 0.551 5.801 4406 Z= 0.280 Chirality : 0.038 0.127 510 Planarity : 0.004 0.047 526 Dihedral : 7.332 76.998 446 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.52 % Allowed : 21.69 % Favored : 73.80 % 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: 2.01 (0.44), residues: 380 helix: 1.91 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -1.90 (0.78), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 107 HIS 0.001 0.000 HIS A 358 PHE 0.024 0.002 PHE A 84 TYR 0.012 0.001 TYR A 438 ARG 0.001 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.302 Fit side-chains REVERT: A 155 TYR cc_start: 0.8594 (m-10) cc_final: 0.8204 (m-10) REVERT: A 424 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6668 (tt) outliers start: 15 outliers final: 8 residues processed: 43 average time/residue: 0.1781 time to fit residues: 9.2724 Evaluate side-chains 40 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 31 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 409 ILE Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.5980 chunk 31 optimal weight: 0.5980 chunk 16 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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 = 0.3713 r_free = 0.3713 target = 0.153207 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.130922 restraints weight = 3563.312| |-----------------------------------------------------------------------------| r_work (start): 0.3278 rms_B_bonded: 1.59 r_work: 0.3149 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 3.87 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.1249 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 3234 Z= 0.264 Angle : 0.548 5.770 4406 Z= 0.279 Chirality : 0.038 0.125 510 Planarity : 0.004 0.045 526 Dihedral : 7.284 78.123 446 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.33 % Allowed : 20.78 % Favored : 72.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.43), residues: 380 helix: 1.87 (0.29), residues: 320 sheet: None (None), residues: 0 loop : -2.02 (0.77), residues: 60 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 358 PHE 0.025 0.001 PHE A 84 TYR 0.012 0.001 TYR A 438 ARG 0.001 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 33 time to evaluate : 0.340 Fit side-chains REVERT: A 424 LEU cc_start: 0.6987 (OUTLIER) cc_final: 0.6743 (tt) outliers start: 21 outliers final: 14 residues processed: 49 average time/residue: 0.1761 time to fit residues: 10.5358 Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.308 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 122 MET Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 419 SER Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 14 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 17 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 34 optimal weight: 0.1980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3572 r_free = 0.3572 target = 0.142495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.117463 restraints weight = 3601.371| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 1.80 r_work: 0.3146 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.3002 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 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 : 0.003 0.042 3234 Z= 0.217 Angle : 0.520 6.150 4406 Z= 0.263 Chirality : 0.037 0.125 510 Planarity : 0.004 0.045 526 Dihedral : 7.234 79.234 446 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.42 % Allowed : 22.29 % Favored : 72.29 % 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: 2.01 (0.43), residues: 380 helix: 1.91 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.96 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.024 0.001 PHE A 84 TYR 0.012 0.001 TYR A 438 ARG 0.001 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 32 time to evaluate : 0.333 Fit side-chains REVERT: A 119 MET cc_start: 0.8570 (mmt) cc_final: 0.8192 (mmt) REVERT: A 155 TYR cc_start: 0.8565 (m-10) cc_final: 0.8201 (m-10) REVERT: A 424 LEU cc_start: 0.6915 (OUTLIER) cc_final: 0.6672 (tt) outliers start: 18 outliers final: 9 residues processed: 45 average time/residue: 0.1843 time to fit residues: 10.0856 Evaluate side-chains 41 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 31 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 19 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 8 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.141831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.116681 restraints weight = 3704.669| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 1.83 r_work: 0.3137 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.2992 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2992 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 moved from start: 0.1414 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3234 Z= 0.231 Angle : 0.518 5.736 4406 Z= 0.263 Chirality : 0.037 0.121 510 Planarity : 0.004 0.044 526 Dihedral : 7.262 80.402 446 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 5.42 % Allowed : 22.89 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.43), residues: 380 helix: 1.90 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -2.00 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.024 0.001 PHE A 84 TYR 0.012 0.001 TYR A 438 ARG 0.001 0.000 ARG A 268 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 33 time to evaluate : 0.267 Fit side-chains REVERT: A 26 ARG cc_start: 0.4781 (ttt180) cc_final: 0.4567 (ttt180) REVERT: A 119 MET cc_start: 0.8565 (mmt) cc_final: 0.8211 (mmt) REVERT: A 155 TYR cc_start: 0.8582 (m-10) cc_final: 0.8215 (m-10) REVERT: A 422 ARG cc_start: 0.6507 (mtm180) cc_final: 0.6119 (tmt170) REVERT: A 424 LEU cc_start: 0.6958 (OUTLIER) cc_final: 0.6712 (tt) outliers start: 18 outliers final: 13 residues processed: 45 average time/residue: 0.2032 time to fit residues: 10.8273 Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 32 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 180 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 12 optimal weight: 2.9990 chunk 30 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 32 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 18 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 overall best weight: 0.4980 ------------------------------------------------------------------------------- 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 = 0.3573 r_free = 0.3573 target = 0.142438 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.117791 restraints weight = 3606.542| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 1.79 r_work: 0.3154 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.3009 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.1480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3234 Z= 0.214 Angle : 0.521 7.910 4406 Z= 0.260 Chirality : 0.037 0.117 510 Planarity : 0.004 0.044 526 Dihedral : 7.281 81.512 446 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 4.52 % Allowed : 23.49 % Favored : 71.99 % 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: 2.06 (0.44), residues: 380 helix: 1.95 (0.29), residues: 321 sheet: None (None), residues: 0 loop : -1.96 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.023 0.001 PHE A 84 TYR 0.012 0.001 TYR A 438 ARG 0.001 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 31 time to evaluate : 0.341 Fit side-chains REVERT: A 26 ARG cc_start: 0.4751 (ttt180) cc_final: 0.4488 (ttt180) REVERT: A 119 MET cc_start: 0.8559 (mmt) cc_final: 0.8212 (mmt) REVERT: A 155 TYR cc_start: 0.8624 (m-10) cc_final: 0.8265 (m-10) REVERT: A 422 ARG cc_start: 0.6462 (mtm180) cc_final: 0.6105 (tmt170) REVERT: A 424 LEU cc_start: 0.6979 (OUTLIER) cc_final: 0.6739 (tt) outliers start: 15 outliers final: 12 residues processed: 41 average time/residue: 0.1869 time to fit residues: 9.2668 Evaluate side-chains 44 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 31 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 GLU Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 8 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.3582 r_free = 0.3582 target = 0.142384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.118313 restraints weight = 3624.695| |-----------------------------------------------------------------------------| r_work (start): 0.3267 rms_B_bonded: 1.75 r_work: 0.3143 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.2998 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2998 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7589 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3234 Z= 0.238 Angle : 0.531 7.170 4406 Z= 0.267 Chirality : 0.037 0.131 510 Planarity : 0.004 0.044 526 Dihedral : 7.385 82.296 446 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 4.52 % Allowed : 23.80 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.43), residues: 380 helix: 1.94 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.96 (0.79), residues: 59 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.024 0.001 PHE A 84 TYR 0.012 0.001 TYR A 438 ARG 0.001 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.355 Fit side-chains REVERT: A 26 ARG cc_start: 0.4890 (ttt180) cc_final: 0.4635 (ttt180) REVERT: A 155 TYR cc_start: 0.8591 (m-10) cc_final: 0.8219 (m-10) REVERT: A 422 ARG cc_start: 0.6513 (mtm180) cc_final: 0.6164 (tmt170) REVERT: A 424 LEU cc_start: 0.7019 (OUTLIER) cc_final: 0.6773 (tt) outliers start: 15 outliers final: 12 residues processed: 42 average time/residue: 0.1872 time to fit residues: 9.5729 Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 32 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 27 optimal weight: 0.8980 chunk 4 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 431 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.140812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.116081 restraints weight = 3637.516| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 1.82 r_work: 0.3143 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2999 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7571 moved from start: 0.1560 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3234 Z= 0.229 Angle : 0.525 6.937 4406 Z= 0.264 Chirality : 0.037 0.116 510 Planarity : 0.004 0.044 526 Dihedral : 7.457 83.226 446 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.52 % Allowed : 24.10 % Favored : 71.39 % 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: 2.09 (0.43), residues: 380 helix: 1.93 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -1.82 (0.80), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.024 0.002 PHE A 84 TYR 0.012 0.001 TYR A 438 ARG 0.001 0.000 ARG A 157 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.336 Fit side-chains REVERT: A 26 ARG cc_start: 0.4827 (ttt180) cc_final: 0.4500 (ttt180) REVERT: A 119 MET cc_start: 0.8595 (mmp) cc_final: 0.8162 (mmt) REVERT: A 155 TYR cc_start: 0.8597 (m-10) cc_final: 0.8224 (m-10) REVERT: A 422 ARG cc_start: 0.6487 (mtm180) cc_final: 0.6144 (tmt170) REVERT: A 424 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6761 (tt) outliers start: 15 outliers final: 14 residues processed: 42 average time/residue: 0.1817 time to fit residues: 9.2741 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 21 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 12 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.139719 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.115008 restraints weight = 3597.264| |-----------------------------------------------------------------------------| r_work (start): 0.3263 rms_B_bonded: 1.80 r_work: 0.3139 rms_B_bonded: 2.57 restraints_weight: 0.5000 r_work: 0.2993 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7616 moved from start: 0.1569 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3234 Z= 0.257 Angle : 0.540 6.867 4406 Z= 0.272 Chirality : 0.038 0.120 510 Planarity : 0.004 0.044 526 Dihedral : 7.622 83.849 446 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 5.12 % Allowed : 23.49 % Favored : 71.39 % 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: 2.00 (0.43), residues: 380 helix: 1.88 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -1.84 (0.79), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.001 0.000 HIS A 27 PHE 0.024 0.001 PHE A 84 TYR 0.012 0.001 TYR A 438 ARG 0.001 0.000 ARG A 157 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 760 Ramachandran restraints generated. 380 Oldfield, 0 Emsley, 380 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 32 time to evaluate : 0.296 Fit side-chains REVERT: A 26 ARG cc_start: 0.4975 (ttt180) cc_final: 0.4683 (ttt180) REVERT: A 119 MET cc_start: 0.8620 (mmp) cc_final: 0.8189 (mmt) REVERT: A 155 TYR cc_start: 0.8627 (m-10) cc_final: 0.8246 (m-10) REVERT: A 422 ARG cc_start: 0.6546 (mtm180) cc_final: 0.6197 (tmt170) REVERT: A 424 LEU cc_start: 0.7034 (OUTLIER) cc_final: 0.6806 (tt) outliers start: 17 outliers final: 14 residues processed: 44 average time/residue: 0.1770 time to fit residues: 9.5273 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 32 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 VAL Chi-restraints excluded: chain A residue 80 LEU Chi-restraints excluded: chain A residue 86 LEU Chi-restraints excluded: chain A residue 88 ASP Chi-restraints excluded: chain A residue 134 ILE Chi-restraints excluded: chain A residue 143 LEU Chi-restraints excluded: chain A residue 177 VAL Chi-restraints excluded: chain A residue 254 MET Chi-restraints excluded: chain A residue 285 VAL Chi-restraints excluded: chain A residue 329 ILE Chi-restraints excluded: chain A residue 421 VAL Chi-restraints excluded: chain A residue 424 LEU Chi-restraints excluded: chain A residue 428 VAL Chi-restraints excluded: chain A residue 452 LEU Chi-restraints excluded: chain A residue 455 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 36 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.0010 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 chunk 29 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 7 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 overall best weight: 0.4986 ------------------------------------------------------------------------------- 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 = 0.3563 r_free = 0.3563 target = 0.141408 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.116712 restraints weight = 3627.502| |-----------------------------------------------------------------------------| r_work (start): 0.3275 rms_B_bonded: 1.81 r_work: 0.3150 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3006 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.3006 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3234 Z= 0.215 Angle : 0.515 6.561 4406 Z= 0.259 Chirality : 0.037 0.115 510 Planarity : 0.004 0.044 526 Dihedral : 7.655 84.724 446 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 4.82 % Allowed : 23.49 % Favored : 71.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.43), residues: 380 helix: 1.93 (0.28), residues: 322 sheet: None (None), residues: 0 loop : -1.82 (0.80), residues: 58 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 107 HIS 0.002 0.000 HIS A 27 PHE 0.024 0.001 PHE A 84 TYR 0.012 0.001 TYR A 438 ARG 0.001 0.000 ARG A 157 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1867.90 seconds wall clock time: 32 minutes 51.57 seconds (1971.57 seconds total)