Starting phenix.real_space_refine on Mon Feb 10 21:45:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lxx_23578/02_2025/7lxx_23578.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lxx_23578/02_2025/7lxx_23578.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/7lxx_23578/02_2025/7lxx_23578.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lxx_23578/02_2025/7lxx_23578.map" model { file = "/net/cci-nas-00/data/ceres_data/7lxx_23578/02_2025/7lxx_23578.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lxx_23578/02_2025/7lxx_23578.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= 0.029 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 10 5.16 5 C 1724 2.51 5 N 466 2.21 5 O 540 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2740 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 971 Classifications: {'peptide': 126} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 123} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 4 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 777 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 6, 'TRANS': 100} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 940 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 940 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain breaks: 5 Unresolved non-hydrogen bonds: 21 Unresolved non-hydrogen angles: 27 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.17, per 1000 atoms: 1.16 Number of scatterers: 2740 At special positions: 0 Unit cell: (71.4, 86.1, 71.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 10 16.00 O 540 8.00 N 466 7.00 C 1724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.07 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 90 " distance=2.03 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.02 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 149 " " NAG B 1 " - " ASN A 17 " Time building additional restraints: 0.74 Conformation dependent library (CDL) restraints added in 311.6 milliseconds 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 642 Finding SS restraints... Secondary structure from input PDB file: 3 helices and 9 sheets defined 4.3% alpha, 50.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 81 through 85 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.847A pdb=" N ILE H 34 " --> pdb=" O SER H 50 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N SER H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.663A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.669A pdb=" N TYR H 115 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 9 through 11 removed outlier: 6.530A pdb=" N TRP L 37 " --> pdb=" O MET L 49 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'L' and resid 9 through 11 Processing sheet with id=AA6, first strand: chain 'L' and resid 18 through 23 Processing sheet with id=AA7, first strand: chain 'A' and resid 65 through 66 Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.464A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.388A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.646A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 83 through 84 removed outlier: 12.962A pdb=" N PHE A 238 " --> pdb=" O PHE A 135 " (cutoff:3.500A) removed outlier: 12.148A pdb=" N ASN A 137 " --> pdb=" O PHE A 238 " (cutoff:3.500A) removed outlier: 9.535A pdb=" N THR A 240 " --> pdb=" O ASN A 137 " (cutoff:3.500A) removed outlier: 4.948A pdb=" N LEU A 242 " --> pdb=" O PRO A 139 " (cutoff:3.500A) removed outlier: 7.473A pdb=" N GLN A 134 " --> pdb=" O ALA A 163 " (cutoff:3.500A) removed outlier: 6.488A pdb=" N ALA A 163 " --> pdb=" O GLN A 134 " (cutoff:3.500A) removed outlier: 8.600A pdb=" N CYS A 136 " --> pdb=" O SER A 161 " (cutoff:3.500A) removed outlier: 7.818A pdb=" N SER A 161 " --> pdb=" O CYS A 136 " (cutoff:3.500A) removed outlier: 6.809A pdb=" N ASP A 138 " --> pdb=" O VAL A 159 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N VAL A 159 " --> pdb=" O ASP A 138 " (cutoff:3.500A) removed outlier: 7.154A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 4.875A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.479A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) 120 hydrogen bonds defined for protein. 276 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: 0.87 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.33: 719 1.33 - 1.45: 607 1.45 - 1.57: 1465 1.57 - 1.69: 0 1.69 - 1.81: 13 Bond restraints: 2804 Sorted by residual: bond pdb=" C5 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.413 1.464 -0.051 2.00e-02 2.50e+03 6.60e+00 bond pdb=" C5 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.413 1.463 -0.050 2.00e-02 2.50e+03 6.20e+00 bond pdb=" C5 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.413 1.461 -0.048 2.00e-02 2.50e+03 5.70e+00 bond pdb=" CD GLU A 154 " pdb=" OE2 GLU A 154 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.54e+00 bond pdb=" CG ASP H 114 " pdb=" OD2 ASP H 114 " ideal model delta sigma weight residual 1.249 1.204 0.045 1.90e-02 2.77e+03 5.51e+00 ... (remaining 2799 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 3138 1.40 - 2.81: 545 2.81 - 4.21: 89 4.21 - 5.62: 26 5.62 - 7.02: 12 Bond angle restraints: 3810 Sorted by residual: angle pdb=" C ASN A 81 " pdb=" N PRO A 82 " pdb=" CA PRO A 82 " ideal model delta sigma weight residual 120.03 127.05 -7.02 9.90e-01 1.02e+00 5.03e+01 angle pdb=" C ALA L 45 " pdb=" N PRO L 46 " pdb=" CA PRO L 46 " ideal model delta sigma weight residual 119.85 126.55 -6.70 1.01e+00 9.80e-01 4.40e+01 angle pdb=" C ARG L 56 " pdb=" N PRO L 57 " pdb=" CA PRO L 57 " ideal model delta sigma weight residual 119.78 126.60 -6.82 1.03e+00 9.43e-01 4.38e+01 angle pdb=" C ASP A 138 " pdb=" N PRO A 139 " pdb=" CA PRO A 139 " ideal model delta sigma weight residual 120.14 126.93 -6.79 1.06e+00 8.90e-01 4.10e+01 angle pdb=" C THR A 250 " pdb=" N PRO A 251 " pdb=" CA PRO A 251 " ideal model delta sigma weight residual 119.85 126.28 -6.43 1.01e+00 9.80e-01 4.05e+01 ... (remaining 3805 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.98: 1585 14.98 - 29.95: 61 29.95 - 44.93: 11 44.93 - 59.90: 5 59.90 - 74.87: 4 Dihedral angle restraints: 1666 sinusoidal: 660 harmonic: 1006 Sorted by residual: dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 120.22 -27.22 1 1.00e+01 1.00e-02 1.06e+01 dihedral pdb=" CG ARG H 67 " pdb=" CD ARG H 67 " pdb=" NE ARG H 67 " pdb=" CZ ARG H 67 " ideal model delta sinusoidal sigma weight residual 180.00 141.04 38.96 2 1.50e+01 4.44e-03 8.43e+00 dihedral pdb=" CB GLU A 154 " pdb=" CG GLU A 154 " pdb=" CD GLU A 154 " pdb=" OE1 GLU A 154 " ideal model delta sinusoidal sigma weight residual 0.00 74.87 -74.87 1 3.00e+01 1.11e-03 7.88e+00 ... (remaining 1663 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 309 0.061 - 0.121: 95 0.121 - 0.181: 14 0.181 - 0.241: 7 0.241 - 0.302: 2 Chirality restraints: 427 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.48 0.08 2.00e-02 2.50e+03 1.72e+01 chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.06e+01 chirality pdb=" C2 NAG A1301 " pdb=" C1 NAG A1301 " pdb=" C3 NAG A1301 " pdb=" N2 NAG A1301 " both_signs ideal model delta sigma weight residual False -2.49 -2.79 0.30 2.00e-01 2.50e+01 2.28e+00 ... (remaining 424 not shown) Planarity restraints: 481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 1 " -0.353 2.00e-02 2.50e+03 3.06e-01 1.17e+03 pdb=" C7 NAG B 1 " 0.085 2.00e-02 2.50e+03 pdb=" C8 NAG B 1 " -0.123 2.00e-02 2.50e+03 pdb=" N2 NAG B 1 " 0.544 2.00e-02 2.50e+03 pdb=" O7 NAG B 1 " -0.154 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR H 95 " 0.014 2.00e-02 2.50e+03 2.86e-02 8.17e+00 pdb=" C TYR H 95 " -0.049 2.00e-02 2.50e+03 pdb=" O TYR H 95 " 0.019 2.00e-02 2.50e+03 pdb=" N CYS H 96 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE H 29 " 0.025 2.00e-02 2.50e+03 1.52e-02 4.05e+00 pdb=" CG PHE H 29 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE H 29 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 PHE H 29 " -0.013 2.00e-02 2.50e+03 pdb=" CE1 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE H 29 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE H 29 " 0.014 2.00e-02 2.50e+03 ... (remaining 478 not shown) Histogram of nonbonded interaction distances: 2.52 - 3.00: 1519 3.00 - 3.47: 2371 3.47 - 3.95: 4484 3.95 - 4.42: 5187 4.42 - 4.90: 8533 Nonbonded interactions: 22094 Sorted by model distance: nonbonded pdb=" OD2 ASP H 73 " pdb=" NZ LYS H 76 " model vdw 2.519 3.120 nonbonded pdb=" N ASP H 62 " pdb=" OD1 ASP H 62 " model vdw 2.529 3.120 nonbonded pdb=" O THR A 250 " pdb=" OG1 THR A 250 " model vdw 2.573 3.040 nonbonded pdb=" N ASN L 33 " pdb=" OD1 ASN L 33 " model vdw 2.579 3.120 nonbonded pdb=" N LYS H 104 " pdb=" N TRP H 105 " model vdw 2.582 2.560 ... (remaining 22089 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.290 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: 0.110 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.370 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.520 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 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 : 0.012 0.052 2804 Z= 0.813 Angle : 1.193 7.023 3810 Z= 0.796 Chirality : 0.064 0.302 427 Planarity : 0.015 0.306 479 Dihedral : 9.984 74.874 1015 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 0.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 1.75 % Favored : 98.25 % 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: 0.69 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.72 (0.40), residues: 154 loop : 0.35 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.004 TRP L 101 HIS 0.002 0.001 HIS A 66 PHE 0.025 0.004 PHE H 29 TYR 0.025 0.004 TYR H 103 ARG 0.004 0.001 ARG A 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 86 time to evaluate : 0.282 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 86 average time/residue: 0.6933 time to fit residues: 61.9794 Evaluate side-chains 61 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 61 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.0870 chunk 25 optimal weight: 0.0980 chunk 13 optimal weight: 0.3980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.0980 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 0.0770 chunk 9 optimal weight: 0.5980 chunk 24 optimal weight: 0.0570 overall best weight: 0.0834 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN L 33 ASN A 99 ASN A 137 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.143868 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3549 r_free = 0.3549 target = 0.136225 restraints weight = 3525.948| |-----------------------------------------------------------------------------| r_work (start): 0.3536 rms_B_bonded: 1.17 r_work: 0.3483 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3396 rms_B_bonded: 2.67 restraints_weight: 0.2500 r_work (final): 0.3396 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.1785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 2804 Z= 0.170 Angle : 0.603 9.143 3810 Z= 0.314 Chirality : 0.044 0.186 427 Planarity : 0.004 0.034 479 Dihedral : 6.147 57.023 459 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 3.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.81 % Allowed : 11.93 % Favored : 85.26 % 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: 0.62 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.90 (0.40), residues: 152 loop : 0.06 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 116 HIS 0.002 0.001 HIS L 41 PHE 0.012 0.002 PHE H 29 TYR 0.016 0.002 TYR A 248 ARG 0.006 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.282 Fit side-chains REVERT: H 19 ARG cc_start: 0.8043 (ttt90) cc_final: 0.7842 (ttm170) REVERT: L 84 ASP cc_start: 0.8102 (m-30) cc_final: 0.7874 (m-30) outliers start: 8 outliers final: 4 residues processed: 71 average time/residue: 0.7281 time to fit residues: 53.7457 Evaluate side-chains 66 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 62 time to evaluate : 0.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 5 optimal weight: 0.0570 chunk 32 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 15 optimal weight: 0.0070 chunk 29 optimal weight: 0.0870 chunk 3 optimal weight: 0.2980 overall best weight: 0.2294 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN L 33 ASN ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3586 r_free = 0.3586 target = 0.139422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.131703 restraints weight = 3546.586| |-----------------------------------------------------------------------------| r_work (start): 0.3495 rms_B_bonded: 1.15 r_work: 0.3442 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3356 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3356 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2804 Z= 0.239 Angle : 0.592 7.424 3810 Z= 0.302 Chirality : 0.044 0.182 427 Planarity : 0.004 0.037 479 Dihedral : 5.749 49.801 459 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 5.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.79 % Favored : 98.21 % Rotamer: Outliers : 3.51 % Allowed : 12.98 % Favored : 83.51 % 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: 0.43 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.80 (0.41), residues: 152 loop : -0.09 (0.48), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.013 0.002 PHE A 133 TYR 0.019 0.002 TYR A 248 ARG 0.007 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.305 Fit side-chains REVERT: H 52 SER cc_start: 0.8903 (p) cc_final: 0.8604 (t) REVERT: L 84 ASP cc_start: 0.8165 (m-30) cc_final: 0.7942 (m-30) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 0.7317 time to fit residues: 52.5653 Evaluate side-chains 68 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 11 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 12 optimal weight: 0.0060 chunk 32 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 overall best weight: 0.3196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN L 41 HIS ** A 239 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3552 r_free = 0.3552 target = 0.136274 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.128501 restraints weight = 3596.798| |-----------------------------------------------------------------------------| r_work (start): 0.3461 rms_B_bonded: 1.15 r_work: 0.3407 rms_B_bonded: 1.38 restraints_weight: 0.5000 r_work: 0.3322 rms_B_bonded: 2.54 restraints_weight: 0.2500 r_work (final): 0.3322 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7908 moved from start: 0.3082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 2804 Z= 0.293 Angle : 0.616 7.565 3810 Z= 0.317 Chirality : 0.045 0.214 427 Planarity : 0.004 0.041 479 Dihedral : 5.559 37.056 459 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer: Outliers : 4.91 % Allowed : 13.33 % Favored : 81.75 % 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: 0.19 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.57 (0.42), residues: 152 loop : -0.19 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 64 HIS 0.005 0.001 HIS H 35 PHE 0.015 0.002 PHE H 29 TYR 0.020 0.002 TYR A 248 ARG 0.006 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 0.284 Fit side-chains REVERT: L 84 ASP cc_start: 0.8271 (m-30) cc_final: 0.8057 (m-30) REVERT: A 20 THR cc_start: 0.8577 (p) cc_final: 0.8363 (p) REVERT: A 153 MET cc_start: 0.8243 (mtt) cc_final: 0.8042 (mtt) outliers start: 14 outliers final: 9 residues processed: 74 average time/residue: 0.7543 time to fit residues: 58.0468 Evaluate side-chains 71 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 46 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 83 MET Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 10 optimal weight: 0.0980 chunk 2 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 0.1980 chunk 20 optimal weight: 0.0870 chunk 3 optimal weight: 0.1980 chunk 8 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 24 optimal weight: 0.0870 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 overall best weight: 0.1336 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 84 ASN H 118 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3492 r_free = 0.3492 target = 0.130972 restraints weight = 3588.476| |-----------------------------------------------------------------------------| r_work (start): 0.3490 rms_B_bonded: 1.18 r_work: 0.3437 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3352 rms_B_bonded: 2.60 restraints_weight: 0.2500 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.3190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2804 Z= 0.166 Angle : 0.550 7.361 3810 Z= 0.286 Chirality : 0.043 0.204 427 Planarity : 0.004 0.041 479 Dihedral : 4.949 32.539 459 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 5.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 3.86 % Allowed : 16.14 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.52 (0.42), residues: 152 loop : -0.19 (0.47), residues: 184 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 101 HIS 0.002 0.000 HIS H 35 PHE 0.010 0.001 PHE A 238 TYR 0.019 0.001 TYR A 248 ARG 0.008 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 66 time to evaluate : 0.275 Fit side-chains REVERT: H 52 SER cc_start: 0.8965 (p) cc_final: 0.8642 (t) REVERT: L 84 ASP cc_start: 0.8212 (m-30) cc_final: 0.7995 (m-30) REVERT: A 20 THR cc_start: 0.8473 (p) cc_final: 0.8236 (p) outliers start: 11 outliers final: 6 residues processed: 72 average time/residue: 0.7622 time to fit residues: 57.0141 Evaluate side-chains 66 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 60 time to evaluate : 0.303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.0770 chunk 23 optimal weight: 0.6980 chunk 26 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 6 optimal weight: 0.7980 chunk 27 optimal weight: 0.0980 chunk 2 optimal weight: 0.9990 chunk 3 optimal weight: 0.0970 overall best weight: 0.3136 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3542 r_free = 0.3542 target = 0.135052 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.127759 restraints weight = 3643.486| |-----------------------------------------------------------------------------| r_work (start): 0.3452 rms_B_bonded: 1.13 r_work: 0.3399 rms_B_bonded: 1.33 restraints_weight: 0.5000 r_work: 0.3314 rms_B_bonded: 2.45 restraints_weight: 0.2500 r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.3391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 2804 Z= 0.285 Angle : 0.596 7.662 3810 Z= 0.311 Chirality : 0.045 0.248 427 Planarity : 0.005 0.049 479 Dihedral : 5.244 31.089 459 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 3.51 % Allowed : 17.54 % Favored : 78.95 % 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: 0.03 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.37 (0.43), residues: 154 loop : -0.21 (0.48), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.002 PHE H 29 TYR 0.017 0.002 TYR A 248 ARG 0.011 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 68 time to evaluate : 0.266 Fit side-chains REVERT: H 52 SER cc_start: 0.9015 (p) cc_final: 0.8661 (t) REVERT: A 20 THR cc_start: 0.8515 (p) cc_final: 0.8249 (p) REVERT: A 153 MET cc_start: 0.8233 (mtt) cc_final: 0.8020 (mtt) outliers start: 10 outliers final: 8 residues processed: 74 average time/residue: 0.7484 time to fit residues: 57.5717 Evaluate side-chains 73 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 7 optimal weight: 0.8980 chunk 2 optimal weight: 0.1980 chunk 26 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 3 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 0.0970 chunk 4 optimal weight: 0.9990 overall best weight: 0.4178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN A 122 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.133662 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3435 r_free = 0.3435 target = 0.126419 restraints weight = 3679.328| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 1.11 r_work: 0.3387 rms_B_bonded: 1.32 restraints_weight: 0.5000 r_work: 0.3301 rms_B_bonded: 2.43 restraints_weight: 0.2500 r_work (final): 0.3301 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7938 moved from start: 0.3544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 2804 Z= 0.353 Angle : 0.630 7.920 3810 Z= 0.329 Chirality : 0.047 0.280 427 Planarity : 0.005 0.050 479 Dihedral : 5.873 39.419 459 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.21 % Allowed : 18.25 % Favored : 77.54 % 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: -0.19 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.18 (0.43), residues: 154 loop : -0.31 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP A 258 HIS 0.005 0.001 HIS H 35 PHE 0.016 0.002 PHE H 29 TYR 0.016 0.002 TYR H 95 ARG 0.010 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 69 time to evaluate : 0.277 Fit side-chains REVERT: A 102 ARG cc_start: 0.8570 (mmt90) cc_final: 0.8350 (mmt90) REVERT: A 153 MET cc_start: 0.8266 (mtt) cc_final: 0.7996 (mtt) outliers start: 12 outliers final: 8 residues processed: 75 average time/residue: 0.7783 time to fit residues: 60.5108 Evaluate side-chains 76 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 68 time to evaluate : 0.263 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 73 ASP Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 1 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 25 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 31 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 11 optimal weight: 0.0870 chunk 12 optimal weight: 0.8980 chunk 26 optimal weight: 0.3980 overall best weight: 0.3958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3503 r_free = 0.3503 target = 0.132064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.124395 restraints weight = 3646.611| |-----------------------------------------------------------------------------| r_work (start): 0.3436 rms_B_bonded: 1.11 r_work: 0.3384 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3300 rms_B_bonded: 2.41 restraints_weight: 0.2500 r_work (final): 0.3300 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7927 moved from start: 0.3614 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 2804 Z= 0.342 Angle : 0.638 7.856 3810 Z= 0.332 Chirality : 0.047 0.273 427 Planarity : 0.005 0.049 479 Dihedral : 5.934 41.628 459 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer: Outliers : 3.86 % Allowed : 19.65 % Favored : 76.49 % 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: -0.28 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.12 (0.43), residues: 154 loop : -0.38 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 258 HIS 0.004 0.001 HIS H 35 PHE 0.017 0.002 PHE H 29 TYR 0.016 0.002 TYR H 95 ARG 0.008 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 67 time to evaluate : 0.303 Fit side-chains REVERT: A 153 MET cc_start: 0.8345 (mtt) cc_final: 0.8068 (mtt) outliers start: 11 outliers final: 10 residues processed: 73 average time/residue: 0.7898 time to fit residues: 59.8008 Evaluate side-chains 75 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 118 LEU Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 26 optimal weight: 0.6980 chunk 15 optimal weight: 0.6980 chunk 0 optimal weight: 0.9990 chunk 25 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 19 optimal weight: 0.2980 chunk 21 optimal weight: 0.7980 chunk 4 optimal weight: 0.0030 chunk 5 optimal weight: 0.2980 chunk 6 optimal weight: 0.7980 chunk 2 optimal weight: 0.3980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.133169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.125513 restraints weight = 3631.630| |-----------------------------------------------------------------------------| r_work (start): 0.3453 rms_B_bonded: 1.10 r_work: 0.3398 rms_B_bonded: 1.35 restraints_weight: 0.5000 r_work: 0.3317 rms_B_bonded: 2.46 restraints_weight: 0.2500 r_work (final): 0.3317 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.3661 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 2804 Z= 0.254 Angle : 0.609 7.656 3810 Z= 0.319 Chirality : 0.046 0.256 427 Planarity : 0.005 0.056 479 Dihedral : 5.736 41.246 459 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.87 % Favored : 96.13 % Rotamer: Outliers : 3.51 % Allowed : 20.70 % Favored : 75.79 % 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: -0.28 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.09 (0.43), residues: 154 loop : -0.35 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.004 0.001 HIS H 35 PHE 0.014 0.002 PHE H 29 TYR 0.015 0.002 TYR A 248 ARG 0.010 0.001 ARG A 102 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 66 time to evaluate : 0.279 Fit side-chains REVERT: A 20 THR cc_start: 0.8482 (p) cc_final: 0.8242 (p) REVERT: A 102 ARG cc_start: 0.8576 (mmt90) cc_final: 0.8349 (mmt90) REVERT: A 153 MET cc_start: 0.8279 (mtt) cc_final: 0.8041 (mtt) outliers start: 10 outliers final: 9 residues processed: 72 average time/residue: 0.7914 time to fit residues: 59.0893 Evaluate side-chains 74 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 65 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 64 VAL Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain H residue 114 ASP Chi-restraints excluded: chain H residue 124 VAL Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 22 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 5 optimal weight: 0.9990 chunk 15 optimal weight: 0.0020 chunk 28 optimal weight: 0.0980 chunk 31 optimal weight: 0.0770 chunk 23 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 4 optimal weight: 0.0070 chunk 10 optimal weight: 0.6980 overall best weight: 0.0764 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN H 118 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138095 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3480 r_free = 0.3480 target = 0.129488 restraints weight = 3538.495| |-----------------------------------------------------------------------------| r_work (start): 0.3485 rms_B_bonded: 1.28 r_work: 0.3423 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 2.86 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2804 Z= 0.161 Angle : 0.568 7.481 3810 Z= 0.298 Chirality : 0.043 0.230 427 Planarity : 0.004 0.049 479 Dihedral : 5.255 36.428 459 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 2.81 % Allowed : 22.11 % Favored : 75.09 % 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: -0.21 (0.47), residues: 336 helix: None (None), residues: 0 sheet: 0.13 (0.43), residues: 154 loop : -0.28 (0.47), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 101 HIS 0.003 0.001 HIS H 35 PHE 0.011 0.001 PHE A 238 TYR 0.014 0.001 TYR A 248 ARG 0.010 0.001 ARG A 102 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 672 Ramachandran restraints generated. 336 Oldfield, 0 Emsley, 336 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 65 time to evaluate : 0.317 Fit side-chains REVERT: H 52 SER cc_start: 0.9004 (p) cc_final: 0.8678 (t) REVERT: A 20 THR cc_start: 0.8470 (p) cc_final: 0.8221 (p) REVERT: A 153 MET cc_start: 0.8253 (mtt) cc_final: 0.8004 (mtt) outliers start: 8 outliers final: 6 residues processed: 70 average time/residue: 0.7777 time to fit residues: 56.5001 Evaluate side-chains 70 residues out of total 298 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 64 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 65 LYS Chi-restraints excluded: chain H residue 85 SER Chi-restraints excluded: chain L residue 110 THR Chi-restraints excluded: chain A residue 16 VAL Chi-restraints excluded: chain A residue 83 VAL Chi-restraints excluded: chain A residue 154 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 23 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 7 optimal weight: 0.6980 chunk 29 optimal weight: 0.2980 chunk 14 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 chunk 3 optimal weight: 0.0970 overall best weight: 0.3778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 56 ASN A 137 ASN A 164 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133591 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.124621 restraints weight = 3520.625| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.17 r_work: 0.3361 rms_B_bonded: 1.44 restraints_weight: 0.5000 r_work: 0.3268 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.065 2804 Z= 0.333 Angle : 0.651 9.045 3810 Z= 0.342 Chirality : 0.047 0.271 427 Planarity : 0.005 0.041 479 Dihedral : 5.742 40.943 459 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % Rotamer: Outliers : 3.86 % Allowed : 20.00 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.35 (0.46), residues: 336 helix: None (None), residues: 0 sheet: 0.06 (0.44), residues: 154 loop : -0.41 (0.46), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP A 258 HIS 0.005 0.001 HIS H 35 PHE 0.017 0.002 PHE H 29 TYR 0.016 0.002 TYR H 95 ARG 0.010 0.001 ARG A 102 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2559.54 seconds wall clock time: 46 minutes 17.50 seconds (2777.50 seconds total)