Starting phenix.real_space_refine on Wed Mar 5 17:04:27 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8z7x_39831/03_2025/8z7x_39831.cif Found real_map, /net/cci-nas-00/data/ceres_data/8z7x_39831/03_2025/8z7x_39831.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.36 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8z7x_39831/03_2025/8z7x_39831.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8z7x_39831/03_2025/8z7x_39831.map" model { file = "/net/cci-nas-00/data/ceres_data/8z7x_39831/03_2025/8z7x_39831.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8z7x_39831/03_2025/8z7x_39831.cif" } resolution = 3.36 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= 0.073 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 14 5.16 5 C 1992 2.51 5 N 442 2.21 5 O 507 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 2955 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2937 Number of conformers: 1 Conformer: "" Number of residues, atoms: 376, 2937 Classifications: {'peptide': 376} Incomplete info: {'truncation_to_alanine': 14} Link IDs: {'PTRANS': 13, 'TRANS': 362} Chain breaks: 1 Unresolved non-hydrogen bonds: 63 Unresolved non-hydrogen angles: 76 Unresolved non-hydrogen dihedrals: 57 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'PHE:plan': 2, 'TYR:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 34 Chain: "A" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'VIB': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.46, per 1000 atoms: 0.83 Number of scatterers: 2955 At special positions: 0 Unit cell: (76.424, 58.716, 67.104, 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 14 16.00 O 507 8.00 N 442 7.00 C 1992 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: 0.68 Conformation dependent library (CDL) restraints added in 327.1 milliseconds 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 712 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 81.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.25 Creating SS restraints... Processing helix chain 'A' and resid 13 through 28 Processing helix chain 'A' and resid 35 through 40 Processing helix chain 'A' and resid 47 through 55 Processing helix chain 'A' and resid 56 through 74 removed outlier: 3.842A pdb=" N THR A 60 " --> pdb=" O PHE A 56 " (cutoff:3.500A) removed outlier: 4.152A pdb=" N LEU A 68 " --> pdb=" O LEU A 64 " (cutoff:3.500A) Proline residue: A 69 - end of helix Processing helix chain 'A' and resid 78 through 100 removed outlier: 4.194A pdb=" N VAL A 82 " --> pdb=" O ARG A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 119 removed outlier: 3.620A pdb=" N GLU A 110 " --> pdb=" O MET A 106 " (cutoff:3.500A) removed outlier: 3.587A pdb=" N MET A 115 " --> pdb=" O PHE A 111 " (cutoff:3.500A) Processing helix chain 'A' and resid 119 through 127 removed outlier: 4.423A pdb=" N ILE A 127 " --> pdb=" O TYR A 123 " (cutoff:3.500A) Processing helix chain 'A' and resid 128 through 130 No H-bonds generated for 'chain 'A' and resid 128 through 130' Processing helix chain 'A' and resid 135 through 164 Processing helix chain 'A' and resid 168 through 186 Processing helix chain 'A' and resid 277 through 297 removed outlier: 3.560A pdb=" N ASN A 297 " --> pdb=" O ASN A 293 " (cutoff:3.500A) Processing helix chain 'A' and resid 298 through 307 removed outlier: 3.605A pdb=" N ALA A 307 " --> pdb=" O TRP A 303 " (cutoff:3.500A) Processing helix chain 'A' and resid 315 through 337 removed outlier: 3.502A pdb=" N VAL A 319 " --> pdb=" O TYR A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 366 removed outlier: 3.979A pdb=" N PHE A 352 " --> pdb=" O ALA A 348 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N VAL A 355 " --> pdb=" O VAL A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 369 through 398 removed outlier: 3.651A pdb=" N VAL A 396 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.858A pdb=" N ASN A 397 " --> pdb=" O GLN A 393 " (cutoff:3.500A) removed outlier: 4.121A pdb=" N LEU A 398 " --> pdb=" O ILE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 402 through 426 removed outlier: 3.663A pdb=" N PHE A 412 " --> pdb=" O GLY A 408 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N ILE A 413 " --> pdb=" O ILE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 434 through 437 Processing helix chain 'A' and resid 438 through 458 218 hydrogen bonds defined for protein. 651 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: 0.72 Time building geometry restraints manager: 0.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 838 1.34 - 1.46: 578 1.46 - 1.57: 1601 1.57 - 1.69: 2 1.69 - 1.81: 23 Bond restraints: 3042 Sorted by residual: bond pdb=" C5 VIB A 501 " pdb=" S1 VIB A 501 " ideal model delta sigma weight residual 1.721 1.589 0.132 2.00e-02 2.50e+03 4.35e+01 bond pdb=" C4A VIB A 501 " pdb=" N4A VIB A 501 " ideal model delta sigma weight residual 1.347 1.449 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C4 VIB A 501 " pdb=" N3 VIB A 501 " ideal model delta sigma weight residual 1.385 1.474 -0.089 2.00e-02 2.50e+03 2.00e+01 bond pdb=" C2 VIB A 501 " pdb=" N3 VIB A 501 " ideal model delta sigma weight residual 1.315 1.395 -0.080 2.00e-02 2.50e+03 1.59e+01 bond pdb=" C4 VIB A 501 " pdb=" C5 VIB A 501 " ideal model delta sigma weight residual 1.358 1.416 -0.058 2.00e-02 2.50e+03 8.35e+00 ... (remaining 3037 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.64: 3987 1.64 - 3.27: 131 3.27 - 4.91: 34 4.91 - 6.54: 9 6.54 - 8.18: 6 Bond angle restraints: 4167 Sorted by residual: angle pdb=" C TRP A 303 " pdb=" N ASP A 304 " pdb=" CA ASP A 304 " ideal model delta sigma weight residual 122.38 116.40 5.98 1.81e+00 3.05e-01 1.09e+01 angle pdb=" CD1 LEU A 302 " pdb=" CG LEU A 302 " pdb=" CD2 LEU A 302 " ideal model delta sigma weight residual 110.80 104.00 6.80 2.20e+00 2.07e-01 9.54e+00 angle pdb=" N PHE A 56 " pdb=" CA PHE A 56 " pdb=" C PHE A 56 " ideal model delta sigma weight residual 109.81 116.40 -6.59 2.21e+00 2.05e-01 8.90e+00 angle pdb=" N VAL A 131 " pdb=" CA VAL A 131 " pdb=" C VAL A 131 " ideal model delta sigma weight residual 107.18 112.00 -4.82 1.73e+00 3.34e-01 7.76e+00 angle pdb=" C VAL A 423 " pdb=" N ILE A 424 " pdb=" CA ILE A 424 " ideal model delta sigma weight residual 121.65 117.57 4.08 1.48e+00 4.57e-01 7.58e+00 ... (remaining 4162 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.12: 1555 17.12 - 34.24: 119 34.24 - 51.36: 34 51.36 - 68.49: 1 68.49 - 85.61: 4 Dihedral angle restraints: 1713 sinusoidal: 599 harmonic: 1114 Sorted by residual: dihedral pdb=" CA ARG A 78 " pdb=" C ARG A 78 " pdb=" N TYR A 79 " pdb=" CA TYR A 79 " ideal model delta harmonic sigma weight residual 180.00 -160.09 -19.91 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" CA PRO A 193 " pdb=" C PRO A 193 " pdb=" N LYS A 194 " pdb=" CA LYS A 194 " ideal model delta harmonic sigma weight residual 180.00 162.45 17.55 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" CA VAL A 425 " pdb=" C VAL A 425 " pdb=" N VAL A 426 " pdb=" CA VAL A 426 " ideal model delta harmonic sigma weight residual -180.00 -163.94 -16.06 0 5.00e+00 4.00e-02 1.03e+01 ... (remaining 1710 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 288 0.035 - 0.070: 124 0.070 - 0.105: 54 0.105 - 0.139: 15 0.139 - 0.174: 7 Chirality restraints: 488 Sorted by residual: chirality pdb=" CB ILE A 420 " pdb=" CA ILE A 420 " pdb=" CG1 ILE A 420 " pdb=" CG2 ILE A 420 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.59e-01 chirality pdb=" CB ILE A 437 " pdb=" CA ILE A 437 " pdb=" CG1 ILE A 437 " pdb=" CG2 ILE A 437 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.17 2.00e-01 2.50e+01 7.37e-01 chirality pdb=" CA PHE A 56 " pdb=" N PHE A 56 " pdb=" C PHE A 56 " pdb=" CB PHE A 56 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.27e-01 ... (remaining 485 not shown) Planarity restraints: 502 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 56 " -0.032 5.00e-02 4.00e+02 4.82e-02 3.71e+00 pdb=" N PRO A 57 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 57 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 57 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 51 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C ILE A 51 " -0.030 2.00e-02 2.50e+03 pdb=" O ILE A 51 " 0.011 2.00e-02 2.50e+03 pdb=" N THR A 52 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 281 " 0.009 2.00e-02 2.50e+03 9.41e-03 2.21e+00 pdb=" CG TRP A 281 " -0.025 2.00e-02 2.50e+03 pdb=" CD1 TRP A 281 " 0.013 2.00e-02 2.50e+03 pdb=" CD2 TRP A 281 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 281 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 281 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 281 " 0.006 2.00e-02 2.50e+03 pdb=" CH2 TRP A 281 " -0.001 2.00e-02 2.50e+03 ... (remaining 499 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 249 2.74 - 3.28: 3184 3.28 - 3.82: 5170 3.82 - 4.36: 5733 4.36 - 4.90: 9879 Nonbonded interactions: 24215 Sorted by model distance: nonbonded pdb=" ND2 ASN A 53 " pdb=" OD1 ASN A 432 " model vdw 2.198 3.120 nonbonded pdb=" OE1 GLN A 300 " pdb=" ND2 ASN A 316 " model vdw 2.289 3.120 nonbonded pdb=" OE1 GLN A 438 " pdb=" OH TYR A 442 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR A 61 " pdb=" OD2 ASP A 427 " model vdw 2.324 3.040 nonbonded pdb=" O PRO A 33 " pdb=" NE2 GLN A 300 " model vdw 2.364 3.120 ... (remaining 24210 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: 1.070 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.350 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6785 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 : 0.006 0.132 3042 Z= 0.380 Angle : 0.795 8.177 4167 Z= 0.400 Chirality : 0.049 0.174 488 Planarity : 0.005 0.048 502 Dihedral : 13.906 85.607 1001 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % 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: -0.59 (0.41), residues: 372 helix: 0.33 (0.29), residues: 283 sheet: None (None), residues: 0 loop : -2.57 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 281 HIS 0.001 0.000 HIS A 200 PHE 0.021 0.002 PHE A 189 TYR 0.019 0.002 TYR A 63 ARG 0.001 0.000 ARG A 144 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 45 time to evaluate : 0.276 Fit side-chains REVERT: A 28 MET cc_start: 0.7780 (ttp) cc_final: 0.6942 (tmm) REVERT: A 96 LEU cc_start: 0.8532 (mt) cc_final: 0.8302 (mt) REVERT: A 437 ILE cc_start: 0.7332 (mp) cc_final: 0.7089 (tt) outliers start: 0 outliers final: 0 residues processed: 45 average time/residue: 0.1113 time to fit residues: 6.6178 Evaluate side-chains 39 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.270 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.0970 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.4980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 17 optimal weight: 0.0770 chunk 21 optimal weight: 0.5980 chunk 33 optimal weight: 0.4980 overall best weight: 0.3536 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.204185 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4145 r_free = 0.4145 target = 0.178765 restraints weight = 2993.629| |-----------------------------------------------------------------------------| r_work (start): 0.4140 rms_B_bonded: 1.93 r_work: 0.4035 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3907 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3907 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6892 moved from start: 0.1020 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3042 Z= 0.205 Angle : 0.593 5.710 4167 Z= 0.305 Chirality : 0.041 0.139 488 Planarity : 0.004 0.041 502 Dihedral : 6.145 82.414 411 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 0.98 % Allowed : 8.79 % Favored : 90.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.43), residues: 372 helix: 0.86 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -2.58 (0.60), residues: 82 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 281 HIS 0.002 0.001 HIS A 135 PHE 0.016 0.001 PHE A 407 TYR 0.011 0.001 TYR A 14 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.285 Fit side-chains REVERT: A 38 TYR cc_start: 0.8697 (t80) cc_final: 0.8342 (t80) REVERT: A 96 LEU cc_start: 0.8653 (mt) cc_final: 0.8408 (mt) REVERT: A 137 GLN cc_start: 0.6586 (tt0) cc_final: 0.5536 (pm20) REVERT: A 403 TYR cc_start: 0.6653 (t80) cc_final: 0.6157 (t80) REVERT: A 424 ILE cc_start: 0.6864 (OUTLIER) cc_final: 0.6650 (mp) outliers start: 3 outliers final: 2 residues processed: 49 average time/residue: 0.0900 time to fit residues: 5.9652 Evaluate side-chains 48 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 9 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 10 optimal weight: 0.3980 chunk 22 optimal weight: 1.9990 chunk 0 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 86 GLN ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4295 r_free = 0.4295 target = 0.197892 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.171963 restraints weight = 3009.351| |-----------------------------------------------------------------------------| r_work (start): 0.4048 rms_B_bonded: 1.93 r_work: 0.3946 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3817 rms_B_bonded: 4.89 restraints_weight: 0.2500 r_work (final): 0.3817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3042 Z= 0.268 Angle : 0.619 6.424 4167 Z= 0.319 Chirality : 0.043 0.144 488 Planarity : 0.004 0.040 502 Dihedral : 6.095 80.276 411 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 1.95 % Allowed : 11.73 % Favored : 86.32 % 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: 0.26 (0.43), residues: 372 helix: 0.94 (0.30), residues: 292 sheet: None (None), residues: 0 loop : -2.64 (0.62), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.013 0.002 PHE A 379 TYR 0.010 0.001 TYR A 280 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.280 Fit side-chains REVERT: A 96 LEU cc_start: 0.8717 (mt) cc_final: 0.8411 (mt) REVERT: A 136 TYR cc_start: 0.7085 (t80) cc_final: 0.5966 (t80) REVERT: A 137 GLN cc_start: 0.6635 (tt0) cc_final: 0.5740 (pm20) REVERT: A 403 TYR cc_start: 0.6766 (t80) cc_final: 0.6099 (t80) REVERT: A 420 ILE cc_start: 0.8361 (mp) cc_final: 0.8140 (mp) REVERT: A 424 ILE cc_start: 0.6847 (OUTLIER) cc_final: 0.6562 (mp) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.1299 time to fit residues: 8.1186 Evaluate side-chains 48 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 45 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 9 optimal weight: 0.3980 chunk 36 optimal weight: 1.9990 chunk 32 optimal weight: 0.3980 chunk 27 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.0980 chunk 3 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4305 r_free = 0.4305 target = 0.199113 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4081 r_free = 0.4081 target = 0.173027 restraints weight = 3100.045| |-----------------------------------------------------------------------------| r_work (start): 0.4055 rms_B_bonded: 1.98 r_work: 0.3953 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3824 rms_B_bonded: 4.94 restraints_weight: 0.2500 r_work (final): 0.3824 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6972 moved from start: 0.1591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3042 Z= 0.216 Angle : 0.599 8.881 4167 Z= 0.303 Chirality : 0.041 0.134 488 Planarity : 0.004 0.039 502 Dihedral : 6.062 81.789 411 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 9.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.03 % Favored : 95.97 % Rotamer: Outliers : 2.28 % Allowed : 13.68 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.43), residues: 372 helix: 1.07 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -2.60 (0.63), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.010 0.001 PHE A 90 TYR 0.009 0.001 TYR A 403 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 47 time to evaluate : 0.321 Fit side-chains REVERT: A 28 MET cc_start: 0.8067 (ttp) cc_final: 0.7245 (tmm) REVERT: A 96 LEU cc_start: 0.8718 (mt) cc_final: 0.8433 (mt) REVERT: A 137 GLN cc_start: 0.6581 (tt0) cc_final: 0.5655 (pm20) REVERT: A 403 TYR cc_start: 0.6731 (t80) cc_final: 0.6096 (t80) REVERT: A 424 ILE cc_start: 0.6844 (OUTLIER) cc_final: 0.6556 (mp) REVERT: A 429 ARG cc_start: 0.8137 (mtm-85) cc_final: 0.7891 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 52 average time/residue: 0.1204 time to fit residues: 8.0181 Evaluate side-chains 50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.5980 chunk 35 optimal weight: 0.4980 chunk 0 optimal weight: 0.9990 chunk 5 optimal weight: 0.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 10 optimal weight: 0.6980 chunk 26 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4273 r_free = 0.4273 target = 0.195617 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.169473 restraints weight = 3083.681| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 1.93 r_work: 0.3891 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3759 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3759 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7049 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3042 Z= 0.276 Angle : 0.636 7.188 4167 Z= 0.321 Chirality : 0.042 0.142 488 Planarity : 0.004 0.039 502 Dihedral : 6.071 79.536 411 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer: Outliers : 2.28 % Allowed : 14.66 % Favored : 83.06 % 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: 0.34 (0.43), residues: 372 helix: 0.93 (0.30), residues: 295 sheet: None (None), residues: 0 loop : -2.46 (0.63), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.011 0.002 PHE A 379 TYR 0.011 0.001 TYR A 280 ARG 0.001 0.001 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.296 Fit side-chains REVERT: A 28 MET cc_start: 0.8060 (ttp) cc_final: 0.7197 (tmm) REVERT: A 96 LEU cc_start: 0.8737 (mt) cc_final: 0.8460 (mt) REVERT: A 137 GLN cc_start: 0.6651 (tt0) cc_final: 0.5716 (pm20) REVERT: A 424 ILE cc_start: 0.6873 (OUTLIER) cc_final: 0.6534 (mp) REVERT: A 429 ARG cc_start: 0.8114 (mtm-85) cc_final: 0.7913 (mtm-85) outliers start: 7 outliers final: 4 residues processed: 49 average time/residue: 0.1205 time to fit residues: 7.5704 Evaluate side-chains 47 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 42 time to evaluate : 0.297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.6980 chunk 28 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.197016 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.170510 restraints weight = 3131.239| |-----------------------------------------------------------------------------| r_work (start): 0.4049 rms_B_bonded: 1.97 r_work: 0.3943 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.3814 rms_B_bonded: 4.96 restraints_weight: 0.2500 r_work (final): 0.3814 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7028 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3042 Z= 0.250 Angle : 0.605 6.313 4167 Z= 0.307 Chirality : 0.041 0.136 488 Planarity : 0.004 0.038 502 Dihedral : 6.045 79.866 411 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 3.26 % Allowed : 14.33 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.43), residues: 372 helix: 1.01 (0.30), residues: 294 sheet: None (None), residues: 0 loop : -2.50 (0.63), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.011 0.001 PHE A 439 TYR 0.011 0.001 TYR A 280 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 44 time to evaluate : 0.303 Fit side-chains REVERT: A 28 MET cc_start: 0.7995 (ttp) cc_final: 0.7149 (tmm) REVERT: A 96 LEU cc_start: 0.8724 (mt) cc_final: 0.8451 (mt) REVERT: A 137 GLN cc_start: 0.6625 (tt0) cc_final: 0.5720 (pm20) REVERT: A 403 TYR cc_start: 0.6912 (OUTLIER) cc_final: 0.6405 (t80) REVERT: A 424 ILE cc_start: 0.6916 (OUTLIER) cc_final: 0.6566 (mp) outliers start: 10 outliers final: 5 residues processed: 51 average time/residue: 0.1225 time to fit residues: 8.0388 Evaluate side-chains 50 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 43 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 84 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 0.9980 chunk 0 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 6 optimal weight: 0.9990 chunk 23 optimal weight: 2.9990 chunk 19 optimal weight: 0.0970 chunk 5 optimal weight: 0.0670 chunk 35 optimal weight: 0.1980 chunk 27 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.199953 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.174013 restraints weight = 3042.926| |-----------------------------------------------------------------------------| r_work (start): 0.4056 rms_B_bonded: 1.94 r_work: 0.3953 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3822 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3822 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3042 Z= 0.200 Angle : 0.581 5.639 4167 Z= 0.296 Chirality : 0.040 0.128 488 Planarity : 0.004 0.038 502 Dihedral : 6.014 81.393 411 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.95 % Allowed : 17.26 % Favored : 80.78 % 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: 0.60 (0.43), residues: 372 helix: 1.19 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -2.59 (0.59), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 90 TYR 0.013 0.001 TYR A 76 ARG 0.003 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.278 Fit side-chains REVERT: A 28 MET cc_start: 0.7887 (ttp) cc_final: 0.7149 (tmm) REVERT: A 96 LEU cc_start: 0.8685 (mt) cc_final: 0.8424 (mt) REVERT: A 137 GLN cc_start: 0.6622 (tt0) cc_final: 0.5752 (pm20) REVERT: A 403 TYR cc_start: 0.6784 (t80) cc_final: 0.6277 (t80) REVERT: A 424 ILE cc_start: 0.6921 (OUTLIER) cc_final: 0.6589 (mp) outliers start: 6 outliers final: 3 residues processed: 52 average time/residue: 0.1157 time to fit residues: 7.7173 Evaluate side-chains 49 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 45 time to evaluate : 0.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 27 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 12 optimal weight: 0.0970 chunk 0 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 chunk 22 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4285 r_free = 0.4285 target = 0.197295 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.171299 restraints weight = 3105.187| |-----------------------------------------------------------------------------| r_work (start): 0.4057 rms_B_bonded: 1.92 r_work: 0.3951 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3821 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3821 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3042 Z= 0.253 Angle : 0.608 6.140 4167 Z= 0.312 Chirality : 0.041 0.137 488 Planarity : 0.004 0.037 502 Dihedral : 5.985 79.718 411 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.95 % Allowed : 17.92 % Favored : 80.13 % 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: 0.56 (0.43), residues: 372 helix: 1.15 (0.30), residues: 294 sheet: None (None), residues: 0 loop : -2.64 (0.59), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 439 TYR 0.012 0.001 TYR A 76 ARG 0.002 0.000 ARG A 429 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.311 Fit side-chains REVERT: A 28 MET cc_start: 0.7909 (ttp) cc_final: 0.7078 (tmm) REVERT: A 96 LEU cc_start: 0.8700 (mt) cc_final: 0.8438 (mt) REVERT: A 403 TYR cc_start: 0.6921 (OUTLIER) cc_final: 0.6464 (t80) REVERT: A 424 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6580 (mp) outliers start: 6 outliers final: 4 residues processed: 47 average time/residue: 0.1270 time to fit residues: 7.6663 Evaluate side-chains 47 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 41 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 8 optimal weight: 0.6980 chunk 18 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 316 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4271 r_free = 0.4271 target = 0.195750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.169602 restraints weight = 3097.786| |-----------------------------------------------------------------------------| r_work (start): 0.4024 rms_B_bonded: 1.94 r_work: 0.3919 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3787 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3787 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7046 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3042 Z= 0.276 Angle : 0.627 6.537 4167 Z= 0.322 Chirality : 0.042 0.142 488 Planarity : 0.004 0.037 502 Dihedral : 6.009 77.942 411 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 1.95 % Allowed : 17.92 % Favored : 80.13 % 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: 0.50 (0.43), residues: 372 helix: 1.10 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -2.56 (0.59), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.002 PHE A 439 TYR 0.011 0.001 TYR A 76 ARG 0.001 0.000 ARG A 277 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 42 time to evaluate : 0.307 Fit side-chains REVERT: A 28 MET cc_start: 0.7934 (ttp) cc_final: 0.7354 (tmm) REVERT: A 96 LEU cc_start: 0.8677 (mt) cc_final: 0.8416 (mt) REVERT: A 403 TYR cc_start: 0.7052 (OUTLIER) cc_final: 0.6669 (t80) REVERT: A 424 ILE cc_start: 0.6913 (OUTLIER) cc_final: 0.6575 (mp) outliers start: 6 outliers final: 4 residues processed: 46 average time/residue: 0.1262 time to fit residues: 7.4152 Evaluate side-chains 49 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 43 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 14 optimal weight: 0.7980 chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 0 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 3 optimal weight: 0.0970 chunk 7 optimal weight: 0.5980 chunk 34 optimal weight: 1.9990 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4264 r_free = 0.4264 target = 0.195171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.169486 restraints weight = 3074.373| |-----------------------------------------------------------------------------| r_work (start): 0.4035 rms_B_bonded: 1.91 r_work: 0.3929 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3802 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7042 moved from start: 0.2208 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3042 Z= 0.260 Angle : 0.623 6.161 4167 Z= 0.320 Chirality : 0.042 0.138 488 Planarity : 0.004 0.037 502 Dihedral : 6.028 77.932 411 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 10.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.76 % Favored : 96.24 % Rotamer: Outliers : 2.28 % Allowed : 18.24 % Favored : 79.48 % 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: 0.50 (0.43), residues: 372 helix: 1.09 (0.30), residues: 293 sheet: None (None), residues: 0 loop : -2.54 (0.61), residues: 79 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.013 0.001 PHE A 439 TYR 0.011 0.001 TYR A 76 ARG 0.003 0.001 ARG A 429 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 744 Ramachandran restraints generated. 372 Oldfield, 0 Emsley, 372 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.311 Fit side-chains REVERT: A 28 MET cc_start: 0.7871 (ttp) cc_final: 0.7325 (tmm) REVERT: A 96 LEU cc_start: 0.8658 (mt) cc_final: 0.8398 (mt) REVERT: A 403 TYR cc_start: 0.7088 (OUTLIER) cc_final: 0.6701 (t80) REVERT: A 424 ILE cc_start: 0.6904 (OUTLIER) cc_final: 0.6580 (mp) REVERT: A 429 ARG cc_start: 0.8139 (mtm-85) cc_final: 0.7656 (mtm-85) outliers start: 7 outliers final: 5 residues processed: 46 average time/residue: 0.1346 time to fit residues: 7.8808 Evaluate side-chains 47 residues out of total 321 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 18 ILE Chi-restraints excluded: chain A residue 36 ILE Chi-restraints excluded: chain A residue 302 LEU Chi-restraints excluded: chain A residue 400 VAL Chi-restraints excluded: chain A residue 403 TYR Chi-restraints excluded: chain A residue 422 THR Chi-restraints excluded: chain A residue 424 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.0970 chunk 27 optimal weight: 0.0980 chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 300 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 438 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4292 r_free = 0.4292 target = 0.198294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172842 restraints weight = 3007.772| |-----------------------------------------------------------------------------| r_work (start): 0.4092 rms_B_bonded: 1.91 r_work: 0.3988 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3859 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3859 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6970 moved from start: 0.2212 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3042 Z= 0.204 Angle : 0.584 5.485 4167 Z= 0.300 Chirality : 0.040 0.129 488 Planarity : 0.004 0.037 502 Dihedral : 5.973 80.038 411 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.61 % Allowed : 17.92 % Favored : 79.48 % 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: 0.73 (0.43), residues: 372 helix: 1.23 (0.30), residues: 294 sheet: None (None), residues: 0 loop : -2.39 (0.61), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP A 281 HIS 0.002 0.001 HIS A 364 PHE 0.012 0.001 PHE A 439 TYR 0.013 0.001 TYR A 76 ARG 0.003 0.000 ARG A 429 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1801.08 seconds wall clock time: 31 minutes 37.96 seconds (1897.96 seconds total)