Starting phenix.real_space_refine on Tue Feb 11 04:01:43 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8k1j_36793/02_2025/8k1j_36793.cif Found real_map, /net/cci-nas-00/data/ceres_data/8k1j_36793/02_2025/8k1j_36793.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8k1j_36793/02_2025/8k1j_36793.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8k1j_36793/02_2025/8k1j_36793.map" model { file = "/net/cci-nas-00/data/ceres_data/8k1j_36793/02_2025/8k1j_36793.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8k1j_36793/02_2025/8k1j_36793.cif" } resolution = 3.0 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= 0.100 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: 5 Type Number sf(0) Gaussians K 5 8.98 5 S 32 5.16 5 C 2706 2.51 5 N 616 2.21 5 O 710 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 4069 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "B" Number of atoms: 1921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 242, 1921 Classifications: {'peptide': 242} Link IDs: {'PTRANS': 4, 'TRANS': 237} Chain breaks: 1 Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 110 Unusual residues: {' K': 5, 'Y01': 3} Classifications: {'undetermined': 8} Link IDs: {None: 7} Chain: "B" Number of atoms: 105 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 105 Unusual residues: {'Y01': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Chain: "B" Number of atoms: 6 Number of conformers: 1 Conformer: "" Number of residues, atoms: 6, 6 Classifications: {'water': 6} Link IDs: {None: 5} Time building chain proxies: 3.13, per 1000 atoms: 0.77 Number of scatterers: 4069 At special positions: 0 Unit cell: (69.3, 71.5, 90.2, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) K 5 19.00 S 32 16.00 O 710 8.00 N 616 7.00 C 2706 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: 1.20 Conformation dependent library (CDL) restraints added in 465.4 milliseconds 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 896 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 0 sheets defined 87.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.37 Creating SS restraints... Processing helix chain 'A' and resid 2 through 53 removed outlier: 5.638A pdb=" N ASP A 32 " --> pdb=" O ALA A 28 " (cutoff:3.500A) removed outlier: 5.070A pdb=" N HIS A 33 " --> pdb=" O LEU A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 70 removed outlier: 3.764A pdb=" N ARG A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) removed outlier: 3.755A pdb=" N GLN A 61 " --> pdb=" O GLU A 57 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 75 Processing helix chain 'A' and resid 79 through 92 Processing helix chain 'A' and resid 103 through 147 Proline residue: A 119 - end of helix Processing helix chain 'A' and resid 155 through 183 Processing helix chain 'A' and resid 185 through 198 Processing helix chain 'A' and resid 212 through 217 Processing helix chain 'A' and resid 217 through 243 Processing helix chain 'A' and resid 244 through 247 Processing helix chain 'B' and resid 3 through 53 removed outlier: 5.634A pdb=" N ASP B 32 " --> pdb=" O ALA B 28 " (cutoff:3.500A) removed outlier: 5.069A pdb=" N HIS B 33 " --> pdb=" O LEU B 29 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 70 removed outlier: 3.901A pdb=" N ARG B 60 " --> pdb=" O SER B 56 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N GLN B 61 " --> pdb=" O GLU B 57 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 75 Processing helix chain 'B' and resid 79 through 92 Processing helix chain 'B' and resid 103 through 147 Proline residue: B 119 - end of helix Processing helix chain 'B' and resid 155 through 183 Processing helix chain 'B' and resid 185 through 198 Processing helix chain 'B' and resid 212 through 217 Processing helix chain 'B' and resid 217 through 243 Processing helix chain 'B' and resid 244 through 247 333 hydrogen bonds defined for protein. 981 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 1.35 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: 664 1.33 - 1.45: 1092 1.45 - 1.57: 2352 1.57 - 1.69: 0 1.69 - 1.81: 48 Bond restraints: 4156 Sorted by residual: bond pdb=" C ILE A 118 " pdb=" N PRO A 119 " ideal model delta sigma weight residual 1.335 1.343 -0.007 1.36e-02 5.41e+03 2.94e-01 bond pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 1.457 1.464 -0.007 1.29e-02 6.01e+03 2.64e-01 bond pdb=" C ILE B 118 " pdb=" N PRO B 119 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.43e-01 bond pdb=" C GLU A 70 " pdb=" N PRO A 71 " ideal model delta sigma weight residual 1.335 1.342 -0.007 1.36e-02 5.41e+03 2.42e-01 bond pdb=" CA LYS B 211 " pdb=" CB LYS B 211 " ideal model delta sigma weight residual 1.530 1.538 -0.008 1.69e-02 3.50e+03 2.33e-01 ... (remaining 4151 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.00: 5548 1.00 - 2.00: 75 2.00 - 3.00: 9 3.00 - 4.00: 6 4.00 - 5.00: 6 Bond angle restraints: 5644 Sorted by residual: angle pdb=" C THR A 210 " pdb=" N LYS A 211 " pdb=" CA LYS A 211 " ideal model delta sigma weight residual 121.54 125.68 -4.14 1.91e+00 2.74e-01 4.70e+00 angle pdb=" C THR B 210 " pdb=" N LYS B 211 " pdb=" CA LYS B 211 " ideal model delta sigma weight residual 121.54 125.66 -4.12 1.91e+00 2.74e-01 4.66e+00 angle pdb=" N GLY A 117 " pdb=" CA GLY A 117 " pdb=" C GLY A 117 " ideal model delta sigma weight residual 113.18 116.98 -3.80 2.37e+00 1.78e-01 2.57e+00 angle pdb=" N GLY B 117 " pdb=" CA GLY B 117 " pdb=" C GLY B 117 " ideal model delta sigma weight residual 113.18 116.93 -3.75 2.37e+00 1.78e-01 2.51e+00 angle pdb=" CA TYR A 18 " pdb=" CB TYR A 18 " pdb=" CG TYR A 18 " ideal model delta sigma weight residual 113.90 116.71 -2.81 1.80e+00 3.09e-01 2.44e+00 ... (remaining 5639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 2433 16.20 - 32.39: 211 32.39 - 48.59: 36 48.59 - 64.79: 20 64.79 - 80.99: 12 Dihedral angle restraints: 2712 sinusoidal: 1310 harmonic: 1402 Sorted by residual: dihedral pdb=" CG ARG B 3 " pdb=" CD ARG B 3 " pdb=" NE ARG B 3 " pdb=" CZ ARG B 3 " ideal model delta sinusoidal sigma weight residual 180.00 -139.84 -40.16 2 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" CG ARG A 3 " pdb=" CD ARG A 3 " pdb=" NE ARG A 3 " pdb=" CZ ARG A 3 " ideal model delta sinusoidal sigma weight residual -180.00 -139.85 -40.15 2 1.50e+01 4.44e-03 8.87e+00 dihedral pdb=" CB GLU B 130 " pdb=" CG GLU B 130 " pdb=" CD GLU B 130 " pdb=" OE1 GLU B 130 " ideal model delta sinusoidal sigma weight residual 0.00 80.30 -80.30 1 3.00e+01 1.11e-03 8.87e+00 ... (remaining 2709 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.021: 437 0.021 - 0.043: 96 0.043 - 0.064: 82 0.064 - 0.086: 20 0.086 - 0.107: 15 Chirality restraints: 650 Sorted by residual: chirality pdb=" CA VAL B 76 " pdb=" N VAL B 76 " pdb=" C VAL B 76 " pdb=" CB VAL B 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.86e-01 chirality pdb=" CA VAL A 76 " pdb=" N VAL A 76 " pdb=" C VAL A 76 " pdb=" CB VAL A 76 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.11 2.00e-01 2.50e+01 2.85e-01 chirality pdb=" CA VAL A 206 " pdb=" N VAL A 206 " pdb=" C VAL A 206 " pdb=" CB VAL A 206 " both_signs ideal model delta sigma weight residual False 2.44 2.55 -0.10 2.00e-01 2.50e+01 2.73e-01 ... (remaining 647 not shown) Planarity restraints: 664 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR B 18 " -0.009 2.00e-02 2.50e+03 6.07e-03 7.38e-01 pdb=" CG TYR B 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR B 18 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR B 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" CZ TYR B 18 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 18 " -0.009 2.00e-02 2.50e+03 5.99e-03 7.17e-01 pdb=" CG TYR A 18 " 0.014 2.00e-02 2.50e+03 pdb=" CD1 TYR A 18 " -0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR A 18 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 18 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 18 " 0.000 2.00e-02 2.50e+03 pdb=" CZ TYR A 18 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR A 18 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 113 " 0.006 2.00e-02 2.50e+03 4.21e-03 3.54e-01 pdb=" CG TYR A 113 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR A 113 " 0.002 2.00e-02 2.50e+03 pdb=" CD2 TYR A 113 " -0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 113 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR A 113 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR A 113 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 113 " 0.002 2.00e-02 2.50e+03 ... (remaining 661 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.86: 1426 2.86 - 3.43: 4548 3.43 - 4.00: 7182 4.00 - 4.57: 10541 4.57 - 5.14: 14505 Nonbonded interactions: 38202 Sorted by model distance: nonbonded pdb=" OH TYR A 52 " pdb=" OD2 ASP B 58 " model vdw 2.296 3.040 nonbonded pdb=" OH TYR A 96 " pdb=" OG1 THR A 196 " model vdw 2.298 3.040 nonbonded pdb=" OH TYR B 96 " pdb=" OG1 THR B 196 " model vdw 2.301 3.040 nonbonded pdb=" O TYR A 113 " pdb=" OH TYR B 18 " model vdw 2.323 3.040 nonbonded pdb=" OH TYR A 18 " pdb=" O TYR B 113 " model vdw 2.324 3.040 ... (remaining 38197 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and (resid 2 through 248 or resid 301 through 303)) selection = chain 'B' } 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: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 14.510 Find NCS groups from input model: 0.150 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: 0.010 Load rotamer database and sin/cos tables:13.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 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 : 0.001 0.012 4156 Z= 0.081 Angle : 0.341 4.999 5644 Z= 0.179 Chirality : 0.031 0.107 650 Planarity : 0.002 0.015 664 Dihedral : 13.842 80.987 1816 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 5.90 (0.38), residues: 476 helix: 4.48 (0.22), residues: 384 sheet: None (None), residues: 0 loop : 0.94 (0.85), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 184 HIS 0.002 0.000 HIS A 72 PHE 0.004 0.000 PHE A 135 TYR 0.014 0.001 TYR B 18 ARG 0.001 0.000 ARG A 47 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.410 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 244 LEU cc_start: 0.7254 (tt) cc_final: 0.6627 (tp) REVERT: B 244 LEU cc_start: 0.7241 (tt) cc_final: 0.6615 (tp) outliers start: 0 outliers final: 0 residues processed: 57 average time/residue: 1.7128 time to fit residues: 100.2547 Evaluate side-chains 51 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 14 optimal weight: 9.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.7980 chunk 43 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4196 r_free = 0.4196 target = 0.190908 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146905 restraints weight = 4042.678| |-----------------------------------------------------------------------------| r_work (start): 0.3804 rms_B_bonded: 1.87 r_work: 0.3621 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3621 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7583 moved from start: 0.2052 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4156 Z= 0.214 Angle : 0.486 6.261 5644 Z= 0.266 Chirality : 0.037 0.122 650 Planarity : 0.003 0.014 664 Dihedral : 6.564 46.794 952 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 1.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.23 % Allowed : 10.78 % Favored : 87.99 % 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: 5.29 (0.37), residues: 476 helix: 4.09 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 0.28 (0.78), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP A 184 HIS 0.002 0.001 HIS A 98 PHE 0.012 0.002 PHE B 223 TYR 0.024 0.002 TYR A 85 ARG 0.005 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.472 Fit side-chains revert: symmetry clash REVERT: A 180 GLN cc_start: 0.7668 (tp40) cc_final: 0.7295 (mp10) REVERT: A 244 LEU cc_start: 0.7062 (tt) cc_final: 0.6657 (tp) REVERT: B 180 GLN cc_start: 0.7658 (tp40) cc_final: 0.7280 (mp10) REVERT: B 244 LEU cc_start: 0.7059 (tt) cc_final: 0.6650 (tp) outliers start: 5 outliers final: 5 residues processed: 53 average time/residue: 1.7383 time to fit residues: 94.5289 Evaluate side-chains 54 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 245 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 16 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 32 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 7.9990 chunk 41 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 42 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 = 0.4163 r_free = 0.4163 target = 0.187610 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.137688 restraints weight = 4128.369| |-----------------------------------------------------------------------------| r_work (start): 0.3692 rms_B_bonded: 1.95 r_work: 0.3525 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.3382 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.2735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4156 Z= 0.196 Angle : 0.461 5.484 5644 Z= 0.253 Chirality : 0.036 0.137 650 Planarity : 0.003 0.031 664 Dihedral : 5.740 39.371 952 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 0.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.05 % Favored : 98.95 % Rotamer: Outliers : 2.21 % Allowed : 10.54 % Favored : 87.25 % 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: 5.06 (0.37), residues: 476 helix: 3.96 (0.23), residues: 390 sheet: None (None), residues: 0 loop : 0.02 (0.74), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 184 HIS 0.002 0.000 HIS A 98 PHE 0.010 0.001 PHE B 135 TYR 0.027 0.002 TYR B 85 ARG 0.006 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.452 Fit side-chains REVERT: A 140 LEU cc_start: 0.7138 (OUTLIER) cc_final: 0.6879 (mm) REVERT: A 180 GLN cc_start: 0.7866 (tp40) cc_final: 0.7470 (mp10) REVERT: A 190 TYR cc_start: 0.8887 (t80) cc_final: 0.8513 (t80) REVERT: B 140 LEU cc_start: 0.7172 (OUTLIER) cc_final: 0.6930 (mm) REVERT: B 180 GLN cc_start: 0.7852 (tp40) cc_final: 0.7453 (mp10) REVERT: B 190 TYR cc_start: 0.8869 (t80) cc_final: 0.8480 (t80) outliers start: 9 outliers final: 4 residues processed: 54 average time/residue: 1.6732 time to fit residues: 92.7583 Evaluate side-chains 57 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 116 LEU Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain A residue 245 ARG Chi-restraints excluded: chain B residue 140 LEU Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 1.9990 chunk 23 optimal weight: 0.4980 chunk 45 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 5 optimal weight: 0.9980 chunk 46 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 0 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 158 ASN B 158 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4141 r_free = 0.4141 target = 0.185317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.134297 restraints weight = 4125.174| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 2.00 r_work: 0.3254 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3106 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3106 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.3187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4156 Z= 0.185 Angle : 0.458 4.832 5644 Z= 0.250 Chirality : 0.036 0.123 650 Planarity : 0.003 0.026 664 Dihedral : 5.195 32.403 952 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.45 % Allowed : 10.78 % Favored : 86.76 % 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: 4.95 (0.37), residues: 476 helix: 3.90 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.14 (0.73), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 78 HIS 0.002 0.000 HIS B 98 PHE 0.007 0.001 PHE A 16 TYR 0.021 0.002 TYR B 85 ARG 0.004 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.445 Fit side-chains REVERT: A 39 GLU cc_start: 0.7905 (mt-10) cc_final: 0.7573 (pt0) REVERT: A 140 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7020 (mm) REVERT: A 180 GLN cc_start: 0.7899 (tp40) cc_final: 0.7525 (mp10) REVERT: A 190 TYR cc_start: 0.8964 (t80) cc_final: 0.8569 (t80) REVERT: B 39 GLU cc_start: 0.7904 (mt-10) cc_final: 0.7570 (pt0) REVERT: B 156 MET cc_start: 0.5971 (tpp) cc_final: 0.5635 (tpt) REVERT: B 180 GLN cc_start: 0.7890 (tp40) cc_final: 0.7513 (mp10) REVERT: B 190 TYR cc_start: 0.8950 (t80) cc_final: 0.8609 (t80) outliers start: 10 outliers final: 1 residues processed: 66 average time/residue: 1.7788 time to fit residues: 120.2314 Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 64 time to evaluate : 0.464 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 46 optimal weight: 0.7980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 45 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 = 0.4114 r_free = 0.4114 target = 0.182924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3603 r_free = 0.3603 target = 0.132321 restraints weight = 4253.760| |-----------------------------------------------------------------------------| r_work (start): 0.3316 rms_B_bonded: 1.98 r_work: 0.3171 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3024 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.3469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 4156 Z= 0.212 Angle : 0.474 6.780 5644 Z= 0.261 Chirality : 0.037 0.154 650 Planarity : 0.003 0.026 664 Dihedral : 5.082 34.212 952 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 2.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.26 % Favored : 98.74 % Rotamer: Outliers : 2.21 % Allowed : 12.75 % Favored : 85.05 % 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: 4.76 (0.38), residues: 476 helix: 3.77 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.19 (0.74), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.002 0.000 HIS A 98 PHE 0.010 0.001 PHE B 135 TYR 0.021 0.002 TYR B 85 ARG 0.005 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 64 time to evaluate : 0.380 Fit side-chains REVERT: A 39 GLU cc_start: 0.7879 (mt-10) cc_final: 0.7524 (pt0) REVERT: A 47 ARG cc_start: 0.7000 (ttp80) cc_final: 0.6768 (ttt-90) REVERT: A 140 LEU cc_start: 0.7265 (OUTLIER) cc_final: 0.7031 (mm) REVERT: A 180 GLN cc_start: 0.7842 (tp40) cc_final: 0.7465 (mp10) REVERT: A 190 TYR cc_start: 0.8962 (t80) cc_final: 0.8544 (t80) REVERT: B 39 GLU cc_start: 0.7886 (mt-10) cc_final: 0.7555 (pt0) REVERT: B 180 GLN cc_start: 0.7828 (tp40) cc_final: 0.7450 (mp10) REVERT: B 190 TYR cc_start: 0.8948 (t80) cc_final: 0.8587 (t80) outliers start: 9 outliers final: 2 residues processed: 68 average time/residue: 1.8150 time to fit residues: 126.3790 Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 64 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 27 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 29 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 24 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 11 optimal weight: 0.0770 chunk 40 optimal weight: 0.6980 overall best weight: 0.7140 ------------------------------------------------------------------------------- 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 = 0.4113 r_free = 0.4113 target = 0.182936 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3609 r_free = 0.3609 target = 0.132798 restraints weight = 4105.566| |-----------------------------------------------------------------------------| r_work (start): 0.3329 rms_B_bonded: 1.94 r_work: 0.3183 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3037 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.3037 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 4156 Z= 0.195 Angle : 0.475 7.435 5644 Z= 0.260 Chirality : 0.036 0.162 650 Planarity : 0.003 0.040 664 Dihedral : 4.960 35.290 952 Min Nonbonded Distance : 2.456 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.47 % Allowed : 13.24 % Favored : 85.29 % 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: 4.76 (0.38), residues: 476 helix: 3.76 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.17 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 78 HIS 0.002 0.000 HIS A 98 PHE 0.008 0.001 PHE B 109 TYR 0.017 0.001 TYR B 85 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.436 Fit side-chains REVERT: A 39 GLU cc_start: 0.7814 (mt-10) cc_final: 0.7544 (pt0) REVERT: A 140 LEU cc_start: 0.7231 (OUTLIER) cc_final: 0.6995 (mm) REVERT: A 180 GLN cc_start: 0.7821 (tp40) cc_final: 0.7438 (mp10) REVERT: A 190 TYR cc_start: 0.8968 (t80) cc_final: 0.8606 (t80) REVERT: B 39 GLU cc_start: 0.7855 (mt-10) cc_final: 0.7540 (pt0) REVERT: B 47 ARG cc_start: 0.7079 (ttt-90) cc_final: 0.6829 (ttt-90) REVERT: B 180 GLN cc_start: 0.7811 (tp40) cc_final: 0.7436 (mp10) REVERT: B 190 TYR cc_start: 0.8964 (t80) cc_final: 0.8593 (t80) outliers start: 6 outliers final: 4 residues processed: 66 average time/residue: 1.8009 time to fit residues: 121.6733 Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 4.9990 chunk 32 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 29 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 1.9990 chunk 10 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4118 r_free = 0.4118 target = 0.183098 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132570 restraints weight = 4138.311| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.99 r_work: 0.3309 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4156 Z= 0.186 Angle : 0.482 8.126 5644 Z= 0.262 Chirality : 0.036 0.172 650 Planarity : 0.003 0.029 664 Dihedral : 4.887 36.235 952 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 2.21 % Allowed : 13.73 % Favored : 84.07 % 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: 4.73 (0.38), residues: 476 helix: 3.75 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.21 (0.74), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 184 HIS 0.002 0.000 HIS B 98 PHE 0.009 0.001 PHE B 135 TYR 0.015 0.001 TYR B 85 ARG 0.006 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.384 Fit side-chains REVERT: A 39 GLU cc_start: 0.7792 (mt-10) cc_final: 0.7514 (pt0) REVERT: A 140 LEU cc_start: 0.7157 (OUTLIER) cc_final: 0.6923 (mm) REVERT: A 180 GLN cc_start: 0.7720 (tp40) cc_final: 0.7238 (mp10) REVERT: A 190 TYR cc_start: 0.8949 (t80) cc_final: 0.8567 (t80) REVERT: B 39 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7517 (pt0) REVERT: B 180 GLN cc_start: 0.7717 (tp40) cc_final: 0.7245 (mp10) REVERT: B 190 TYR cc_start: 0.8943 (t80) cc_final: 0.8552 (t80) outliers start: 9 outliers final: 5 residues processed: 68 average time/residue: 1.7981 time to fit residues: 125.1504 Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.518 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 44 optimal weight: 0.9980 chunk 29 optimal weight: 0.1980 chunk 8 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 22 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 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 = 0.4116 r_free = 0.4116 target = 0.182547 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3608 r_free = 0.3608 target = 0.132460 restraints weight = 4074.155| |-----------------------------------------------------------------------------| r_work (start): 0.3454 rms_B_bonded: 1.95 r_work: 0.3310 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.3161 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3161 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7858 moved from start: 0.3745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4156 Z= 0.196 Angle : 0.487 8.548 5644 Z= 0.265 Chirality : 0.036 0.175 650 Planarity : 0.003 0.029 664 Dihedral : 4.813 37.894 952 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 2.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.47 % Allowed : 14.71 % Favored : 83.82 % 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: 4.69 (0.38), residues: 476 helix: 3.75 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.38 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 78 HIS 0.002 0.000 HIS A 98 PHE 0.008 0.001 PHE A 109 TYR 0.013 0.001 TYR B 85 ARG 0.007 0.000 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.396 Fit side-chains REVERT: A 39 GLU cc_start: 0.7764 (mt-10) cc_final: 0.7495 (pt0) REVERT: A 140 LEU cc_start: 0.7161 (OUTLIER) cc_final: 0.6925 (mm) REVERT: A 180 GLN cc_start: 0.7726 (tp40) cc_final: 0.7239 (mp10) REVERT: A 190 TYR cc_start: 0.8953 (t80) cc_final: 0.8568 (t80) REVERT: B 39 GLU cc_start: 0.7837 (mt-10) cc_final: 0.7510 (pt0) REVERT: B 135 PHE cc_start: 0.7866 (t80) cc_final: 0.7588 (t80) REVERT: B 180 GLN cc_start: 0.7715 (tp40) cc_final: 0.7228 (mp10) REVERT: B 190 TYR cc_start: 0.8946 (t80) cc_final: 0.8554 (t80) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 1.8652 time to fit residues: 122.1322 Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4109 r_free = 0.4109 target = 0.181768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.131400 restraints weight = 4140.746| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 1.97 r_work: 0.3290 rms_B_bonded: 2.97 restraints_weight: 0.5000 r_work: 0.3142 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7880 moved from start: 0.3851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4156 Z= 0.216 Angle : 0.495 8.780 5644 Z= 0.272 Chirality : 0.037 0.179 650 Planarity : 0.003 0.030 664 Dihedral : 4.835 39.244 952 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.47 % Allowed : 14.95 % Favored : 83.58 % 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: 4.63 (0.38), residues: 476 helix: 3.71 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.44 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 78 HIS 0.002 0.000 HIS A 98 PHE 0.009 0.001 PHE A 135 TYR 0.013 0.001 TYR B 85 ARG 0.006 0.001 ARG B 137 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.439 Fit side-chains REVERT: A 39 GLU cc_start: 0.7795 (mt-10) cc_final: 0.7522 (pt0) REVERT: A 140 LEU cc_start: 0.7194 (OUTLIER) cc_final: 0.6960 (mm) REVERT: A 180 GLN cc_start: 0.7727 (tp40) cc_final: 0.7231 (mp10) REVERT: A 190 TYR cc_start: 0.8964 (t80) cc_final: 0.8573 (t80) REVERT: B 39 GLU cc_start: 0.7776 (mt-10) cc_final: 0.7474 (pt0) REVERT: B 180 GLN cc_start: 0.7727 (tp40) cc_final: 0.7233 (mp10) REVERT: B 190 TYR cc_start: 0.8959 (t80) cc_final: 0.8565 (t80) outliers start: 6 outliers final: 5 residues processed: 64 average time/residue: 1.8932 time to fit residues: 123.9643 Evaluate side-chains 68 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 62 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain A residue 159 MET Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 159 MET Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 17 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 45 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 44 optimal weight: 0.2980 chunk 38 optimal weight: 6.9990 chunk 36 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4116 r_free = 0.4116 target = 0.182722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3607 r_free = 0.3607 target = 0.132349 restraints weight = 4168.514| |-----------------------------------------------------------------------------| r_work (start): 0.3631 rms_B_bonded: 1.98 r_work: 0.3469 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3325 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.3325 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7839 moved from start: 0.3866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 4156 Z= 0.190 Angle : 0.487 8.718 5644 Z= 0.267 Chirality : 0.036 0.177 650 Planarity : 0.003 0.030 664 Dihedral : 4.768 39.828 952 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 2.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 1.47 % Allowed : 14.95 % Favored : 83.58 % 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: 4.69 (0.38), residues: 476 helix: 3.75 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.37 (0.70), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 184 HIS 0.001 0.000 HIS B 98 PHE 0.008 0.001 PHE B 109 TYR 0.012 0.001 TYR B 85 ARG 0.007 0.000 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 952 Ramachandran restraints generated. 476 Oldfield, 0 Emsley, 476 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 61 time to evaluate : 0.423 Fit side-chains REVERT: A 39 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7523 (pt0) REVERT: A 140 LEU cc_start: 0.7143 (OUTLIER) cc_final: 0.6909 (mm) REVERT: A 156 MET cc_start: 0.5647 (tpp) cc_final: 0.5406 (tpt) REVERT: A 180 GLN cc_start: 0.7679 (tp40) cc_final: 0.7182 (mp10) REVERT: A 190 TYR cc_start: 0.8937 (t80) cc_final: 0.8531 (t80) REVERT: B 39 GLU cc_start: 0.7765 (mt-10) cc_final: 0.7495 (pt0) REVERT: B 135 PHE cc_start: 0.8006 (t80) cc_final: 0.7781 (t80) REVERT: B 180 GLN cc_start: 0.7672 (tp40) cc_final: 0.7171 (mp10) REVERT: B 190 TYR cc_start: 0.8930 (t80) cc_final: 0.8523 (t80) outliers start: 6 outliers final: 3 residues processed: 64 average time/residue: 1.9820 time to fit residues: 129.7856 Evaluate side-chains 66 residues out of total 408 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 VAL Chi-restraints excluded: chain A residue 140 LEU Chi-restraints excluded: chain B residue 115 VAL Chi-restraints excluded: chain B residue 239 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 47 optimal weight: 0.5980 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 37 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 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 = 0.4105 r_free = 0.4105 target = 0.181694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.131858 restraints weight = 4114.164| |-----------------------------------------------------------------------------| r_work (start): 0.3446 rms_B_bonded: 1.91 r_work: 0.3298 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.3152 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3152 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7976 moved from start: 0.3945 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4156 Z= 0.206 Angle : 0.497 8.863 5644 Z= 0.273 Chirality : 0.037 0.178 650 Planarity : 0.003 0.031 664 Dihedral : 4.792 40.882 952 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.10 % Favored : 97.90 % Rotamer: Outliers : 1.47 % Allowed : 15.44 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.62 (0.38), residues: 476 helix: 3.71 (0.24), residues: 390 sheet: None (None), residues: 0 loop : -0.42 (0.69), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 184 HIS 0.002 0.001 HIS B 98 PHE 0.008 0.001 PHE A 135 TYR 0.012 0.001 TYR B 85 ARG 0.006 0.001 ARG B 137 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3661.20 seconds wall clock time: 65 minutes 15.03 seconds (3915.03 seconds total)