Starting phenix.real_space_refine on Thu Mar 6 05:42:32 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9byi_45034/03_2025/9byi_45034_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9byi_45034/03_2025/9byi_45034.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9byi_45034/03_2025/9byi_45034.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9byi_45034/03_2025/9byi_45034.map" model { file = "/net/cci-nas-00/data/ceres_data/9byi_45034/03_2025/9byi_45034_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9byi_45034/03_2025/9byi_45034_trim.cif" } resolution = 2.95 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= 0.001 sd= 0.012 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 3 8.98 5 S 28 5.16 5 C 3042 2.51 5 N 708 2.21 5 O 724 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-5624/modules/chem_data/mon_lib" Total number of atoms: 4505 Number of models: 1 Model: "" Number of chains: 4 Chain: "U" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2107 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 4, 'TRANS': 257} Chain breaks: 1 Chain: "A" Number of atoms: 2107 Number of conformers: 1 Conformer: "" Number of residues, atoms: 262, 2107 Classifications: {'peptide': 262} Link IDs: {'PTRANS': 4, 'TRANS': 257} Chain breaks: 1 Chain: "U" Number of atoms: 144 Number of conformers: 1 Conformer: "" Number of residues, atoms: 14, 144 Unusual residues: {'D12': 4, 'EIC': 1, 'HEX': 2, 'OCT': 6, 'R16': 1} Classifications: {'undetermined': 14} Link IDs: {None: 13} Chain: "A" Number of atoms: 147 Number of conformers: 1 Conformer: "" Number of residues, atoms: 17, 147 Unusual residues: {' K': 3, 'D12': 4, 'EIC': 1, 'HEX': 2, 'OCT': 6, 'R16': 1} Classifications: {'undetermined': 17} Link IDs: {None: 16} Time building chain proxies: 3.74, per 1000 atoms: 0.83 Number of scatterers: 4505 At special positions: 0 Unit cell: (64.5, 77.4, 98.9, 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 3 19.00 S 28 16.00 O 724 8.00 N 708 7.00 C 3042 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: 1.41 Conformation dependent library (CDL) restraints added in 509.2 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 972 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 77.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.34 Creating SS restraints... Processing helix chain 'U' and resid 14 through 64 removed outlier: 3.674A pdb=" N ALA U 40 " --> pdb=" O ALA U 36 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) removed outlier: 5.573A pdb=" N HIS U 45 " --> pdb=" O LEU U 41 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N HIS U 64 " --> pdb=" O PHE U 60 " (cutoff:3.500A) Processing helix chain 'U' and resid 68 through 85 Processing helix chain 'U' and resid 96 through 109 removed outlier: 3.626A pdb=" N SER U 109 " --> pdb=" O GLY U 105 " (cutoff:3.500A) Processing helix chain 'U' and resid 124 through 166 removed outlier: 4.424A pdb=" N SER U 136 " --> pdb=" O LEU U 132 " (cutoff:3.500A) removed outlier: 3.972A pdb=" N SER U 137 " --> pdb=" O VAL U 133 " (cutoff:3.500A) Processing helix chain 'U' and resid 193 through 215 removed outlier: 3.827A pdb=" N MET U 215 " --> pdb=" O CYS U 211 " (cutoff:3.500A) Processing helix chain 'U' and resid 223 through 236 Processing helix chain 'U' and resid 255 through 295 removed outlier: 3.838A pdb=" N PHE U 259 " --> pdb=" O GLY U 255 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ASP U 295 " --> pdb=" O LEU U 291 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 64 removed outlier: 5.849A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.527A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 68 through 84 Processing helix chain 'A' and resid 97 through 109 removed outlier: 3.575A pdb=" N SER A 109 " --> pdb=" O GLY A 105 " (cutoff:3.500A) Processing helix chain 'A' and resid 124 through 166 removed outlier: 4.422A pdb=" N SER A 136 " --> pdb=" O LEU A 132 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N SER A 137 " --> pdb=" O VAL A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 215 removed outlier: 3.669A pdb=" N MET A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 255 through 294 removed outlier: 3.894A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) 331 hydrogen bonds defined for protein. 993 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: 1.06 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 635 1.32 - 1.44: 1325 1.44 - 1.56: 2578 1.56 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4578 Sorted by residual: bond pdb=" C TYR U 102 " pdb=" O TYR U 102 " ideal model delta sigma weight residual 1.236 1.193 0.044 1.26e-02 6.30e+03 1.20e+01 bond pdb=" C2 HEX U 401 " pdb=" C3 HEX U 401 " ideal model delta sigma weight residual 1.524 1.460 0.064 2.00e-02 2.50e+03 1.01e+01 bond pdb=" C2 HEX A 411 " pdb=" C3 HEX A 411 " ideal model delta sigma weight residual 1.524 1.462 0.062 2.00e-02 2.50e+03 9.63e+00 bond pdb=" N VAL A 91 " pdb=" CA VAL A 91 " ideal model delta sigma weight residual 1.455 1.496 -0.040 1.38e-02 5.25e+03 8.61e+00 bond pdb=" N ASP U 96 " pdb=" CA ASP U 96 " ideal model delta sigma weight residual 1.452 1.487 -0.034 1.22e-02 6.72e+03 7.82e+00 ... (remaining 4573 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.47: 5999 2.47 - 4.93: 64 4.93 - 7.40: 6 7.40 - 9.86: 0 9.86 - 12.33: 3 Bond angle restraints: 6072 Sorted by residual: angle pdb=" N ASN A 90 " pdb=" CA ASN A 90 " pdb=" C ASN A 90 " ideal model delta sigma weight residual 111.24 123.57 -12.33 1.38e+00 5.25e-01 7.98e+01 angle pdb=" C ASN A 90 " pdb=" CA ASN A 90 " pdb=" CB ASN A 90 " ideal model delta sigma weight residual 112.09 106.00 6.09 1.54e+00 4.22e-01 1.57e+01 angle pdb=" N GLN A 164 " pdb=" CA GLN A 164 " pdb=" C GLN A 164 " ideal model delta sigma weight residual 111.36 107.21 4.15 1.09e+00 8.42e-01 1.45e+01 angle pdb=" CA TYR U 102 " pdb=" CB TYR U 102 " pdb=" CG TYR U 102 " ideal model delta sigma weight residual 113.90 120.21 -6.31 1.80e+00 3.09e-01 1.23e+01 angle pdb=" C3 HEX U 401 " pdb=" C4 HEX U 401 " pdb=" C5 HEX U 401 " ideal model delta sigma weight residual 113.35 123.56 -10.21 3.00e+00 1.11e-01 1.16e+01 ... (remaining 6067 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.27: 2325 16.27 - 32.54: 239 32.54 - 48.81: 89 48.81 - 65.08: 28 65.08 - 81.35: 3 Dihedral angle restraints: 2684 sinusoidal: 1166 harmonic: 1518 Sorted by residual: dihedral pdb=" CA ASP A 96 " pdb=" C ASP A 96 " pdb=" N PHE A 97 " pdb=" CA PHE A 97 " ideal model delta harmonic sigma weight residual 180.00 155.68 24.32 0 5.00e+00 4.00e-02 2.37e+01 dihedral pdb=" CB GLU U 252 " pdb=" CG GLU U 252 " pdb=" CD GLU U 252 " pdb=" OE1 GLU U 252 " ideal model delta sinusoidal sigma weight residual 0.00 -81.35 81.35 1 3.00e+01 1.11e-03 9.06e+00 dihedral pdb=" N ASN A 90 " pdb=" C ASN A 90 " pdb=" CA ASN A 90 " pdb=" CB ASN A 90 " ideal model delta harmonic sigma weight residual 122.80 130.29 -7.49 0 2.50e+00 1.60e-01 8.98e+00 ... (remaining 2681 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 617 0.073 - 0.146: 27 0.146 - 0.219: 1 0.219 - 0.292: 0 0.292 - 0.365: 1 Chirality restraints: 646 Sorted by residual: chirality pdb=" CA ASN A 90 " pdb=" N ASN A 90 " pdb=" C ASN A 90 " pdb=" CB ASN A 90 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.33e+00 chirality pdb=" CA GLN A 164 " pdb=" N GLN A 164 " pdb=" C GLN A 164 " pdb=" CB GLN A 164 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.46e-01 chirality pdb=" CA GLN A 285 " pdb=" N GLN A 285 " pdb=" C GLN A 285 " pdb=" CB GLN A 285 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.14e-01 ... (remaining 643 not shown) Planarity restraints: 730 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL A 88 " 0.025 2.00e-02 2.50e+03 5.03e-02 2.53e+01 pdb=" C VAL A 88 " -0.087 2.00e-02 2.50e+03 pdb=" O VAL A 88 " 0.033 2.00e-02 2.50e+03 pdb=" N ASP A 89 " 0.030 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG U 94 " -0.013 2.00e-02 2.50e+03 2.60e-02 6.75e+00 pdb=" C ARG U 94 " 0.045 2.00e-02 2.50e+03 pdb=" O ARG U 94 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP U 95 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 217 " 0.020 5.00e-02 4.00e+02 2.97e-02 1.41e+00 pdb=" N PRO A 218 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 218 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 218 " 0.017 5.00e-02 4.00e+02 ... (remaining 727 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.85: 1510 2.85 - 3.42: 4800 3.42 - 4.00: 7333 4.00 - 4.57: 10656 4.57 - 5.14: 15507 Nonbonded interactions: 39806 Sorted by model distance: nonbonded pdb=" OH TYR U 78 " pdb=" OE2 GLU A 79 " model vdw 2.279 3.040 nonbonded pdb=" OE2 GLU U 220 " pdb=" OH TYR U 251 " model vdw 2.290 3.040 nonbonded pdb=" O SER A 236 " pdb=" OG1 THR A 237 " model vdw 2.319 3.040 nonbonded pdb=" O SER U 236 " pdb=" OG1 THR U 237 " model vdw 2.322 3.040 nonbonded pdb=" O SER A 109 " pdb=" OG1 THR A 110 " model vdw 2.349 3.040 ... (remaining 39801 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 14 through 295 or resid 406 through 408 or resid 410 or re \ sid 412 through 414)) selection = (chain 'U' and (resid 14 through 295 or resid 406 through 408 or resid 410 or re \ sid 412 through 414)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.370 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.020 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:13.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8576 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.064 4578 Z= 0.298 Angle : 0.654 12.327 6072 Z= 0.363 Chirality : 0.036 0.365 646 Planarity : 0.003 0.050 730 Dihedral : 15.740 81.350 1712 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 11.04 % Favored : 88.96 % 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: 4.10 (0.39), residues: 516 helix: 3.76 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -2.40 (0.57), residues: 100 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 53 HIS 0.002 0.001 HIS A 250 PHE 0.010 0.001 PHE A 20 TYR 0.010 0.002 TYR A 30 ARG 0.005 0.000 ARG U 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.469 Fit side-chains REVERT: U 191 LYS cc_start: 0.9342 (mttt) cc_final: 0.9104 (pttt) REVERT: A 191 LYS cc_start: 0.9224 (mmtt) cc_final: 0.8996 (tttt) outliers start: 0 outliers final: 0 residues processed: 99 average time/residue: 2.1423 time to fit residues: 218.4362 Evaluate side-chains 56 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.721 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.0010 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 15 optimal weight: 8.9990 chunk 24 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.090320 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2929 r_free = 0.2929 target = 0.071469 restraints weight = 10097.795| |-----------------------------------------------------------------------------| r_work (start): 0.2909 rms_B_bonded: 3.10 r_work: 0.2776 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2776 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1759 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4578 Z= 0.199 Angle : 0.567 7.229 6072 Z= 0.306 Chirality : 0.033 0.132 646 Planarity : 0.003 0.031 730 Dihedral : 13.339 59.534 780 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 1.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.15 % Allowed : 15.09 % Favored : 81.76 % 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: 4.52 (0.39), residues: 516 helix: 4.19 (0.25), residues: 410 sheet: None (None), residues: 0 loop : -2.52 (0.57), residues: 106 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 95 HIS 0.003 0.001 HIS A 64 PHE 0.010 0.001 PHE U 262 TYR 0.020 0.001 TYR U 155 ARG 0.007 0.000 ARG U 62 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 69 time to evaluate : 0.537 Fit side-chains REVERT: U 191 LYS cc_start: 0.9506 (mttt) cc_final: 0.9027 (pttt) REVERT: A 46 GLU cc_start: 0.8716 (OUTLIER) cc_final: 0.8404 (tt0) REVERT: A 191 LYS cc_start: 0.9442 (mmtt) cc_final: 0.8905 (tttt) REVERT: A 293 LYS cc_start: 0.8873 (tppp) cc_final: 0.8643 (tppt) outliers start: 14 outliers final: 5 residues processed: 78 average time/residue: 2.0793 time to fit residues: 167.4449 Evaluate side-chains 64 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 273 TYR Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 247 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 44 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 38 optimal weight: 0.8980 chunk 40 optimal weight: 6.9990 chunk 3 optimal weight: 0.9980 chunk 22 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 overall best weight: 0.5718 ------------------------------------------------------------------------------- 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 = 0.3327 r_free = 0.3327 target = 0.093578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2996 r_free = 0.2996 target = 0.074783 restraints weight = 10068.720| |-----------------------------------------------------------------------------| r_work (start): 0.2979 rms_B_bonded: 3.09 r_work: 0.2846 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4578 Z= 0.158 Angle : 0.509 6.565 6072 Z= 0.273 Chirality : 0.032 0.153 646 Planarity : 0.002 0.021 730 Dihedral : 10.738 59.977 780 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 3.38 % Allowed : 15.32 % Favored : 81.31 % 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: 4.79 (0.39), residues: 516 helix: 4.42 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.49 (0.58), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 95 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE A 262 TYR 0.008 0.001 TYR A 30 ARG 0.003 0.000 ARG U 62 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 67 time to evaluate : 0.596 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8740 (OUTLIER) cc_final: 0.8489 (tt0) REVERT: U 158 LYS cc_start: 0.9021 (tmmt) cc_final: 0.8517 (tppp) REVERT: U 191 LYS cc_start: 0.9482 (mttt) cc_final: 0.9037 (pttt) REVERT: U 213 SER cc_start: 0.8818 (m) cc_final: 0.8153 (t) REVERT: A 46 GLU cc_start: 0.8766 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: A 191 LYS cc_start: 0.9468 (mmtt) cc_final: 0.8959 (tttt) outliers start: 15 outliers final: 7 residues processed: 78 average time/residue: 1.8704 time to fit residues: 152.0824 Evaluate side-chains 63 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 273 TYR Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 8 optimal weight: 0.9980 chunk 43 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 9 optimal weight: 0.5980 chunk 33 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 247 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.092425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.2961 r_free = 0.2961 target = 0.073297 restraints weight = 9947.887| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 3.07 r_work: 0.2806 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8147 moved from start: 0.2409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4578 Z= 0.183 Angle : 0.519 5.816 6072 Z= 0.276 Chirality : 0.032 0.111 646 Planarity : 0.002 0.022 730 Dihedral : 9.335 58.730 780 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 1.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 2.03 % Allowed : 17.79 % Favored : 80.18 % 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: 4.93 (0.40), residues: 516 helix: 4.52 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.43 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.003 0.001 HIS A 64 PHE 0.009 0.001 PHE U 262 TYR 0.020 0.001 TYR U 155 ARG 0.001 0.000 ARG U 62 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: U 158 LYS cc_start: 0.9026 (tmmt) cc_final: 0.8531 (tppp) REVERT: U 191 LYS cc_start: 0.9514 (mttt) cc_final: 0.9049 (pttt) REVERT: A 46 GLU cc_start: 0.8790 (OUTLIER) cc_final: 0.8490 (tt0) REVERT: A 191 LYS cc_start: 0.9484 (mmtt) cc_final: 0.8934 (tttt) outliers start: 9 outliers final: 8 residues processed: 68 average time/residue: 1.3010 time to fit residues: 93.0529 Evaluate side-chains 63 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 273 TYR Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 27 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 24 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 42 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.3308 r_free = 0.3308 target = 0.092091 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2970 r_free = 0.2970 target = 0.073285 restraints weight = 10452.761| |-----------------------------------------------------------------------------| r_work (start): 0.2951 rms_B_bonded: 3.10 r_work: 0.2820 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2820 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4578 Z= 0.179 Angle : 0.518 6.314 6072 Z= 0.275 Chirality : 0.032 0.106 646 Planarity : 0.002 0.021 730 Dihedral : 8.418 59.412 780 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 1.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.25 % Allowed : 17.34 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.99 (0.39), residues: 516 helix: 4.56 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.41 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.003 0.001 HIS A 64 PHE 0.008 0.001 PHE U 262 TYR 0.007 0.001 TYR A 30 ARG 0.001 0.000 ARG U 47 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8768 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: U 158 LYS cc_start: 0.9033 (tmmt) cc_final: 0.8559 (tppp) REVERT: U 191 LYS cc_start: 0.9523 (mttt) cc_final: 0.9063 (pttt) REVERT: U 213 SER cc_start: 0.8836 (m) cc_final: 0.8155 (t) REVERT: A 46 GLU cc_start: 0.8805 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: A 191 LYS cc_start: 0.9520 (mmtt) cc_final: 0.8929 (tttt) REVERT: A 293 LYS cc_start: 0.8798 (tppt) cc_final: 0.8277 (tppp) outliers start: 10 outliers final: 8 residues processed: 69 average time/residue: 1.0960 time to fit residues: 79.3946 Evaluate side-chains 64 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.566 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 273 TYR Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 215 MET Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 33 optimal weight: 0.3980 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 37 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 51 optimal weight: 0.6980 chunk 1 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- 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 = 0.3282 r_free = 0.3282 target = 0.090850 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.071730 restraints weight = 10011.372| |-----------------------------------------------------------------------------| r_work (start): 0.2911 rms_B_bonded: 3.08 r_work: 0.2775 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2775 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.2554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4578 Z= 0.203 Angle : 0.534 6.252 6072 Z= 0.285 Chirality : 0.032 0.101 646 Planarity : 0.002 0.021 730 Dihedral : 8.189 59.395 780 Min Nonbonded Distance : 2.549 Molprobity Statistics. All-atom Clashscore : 1.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 2.25 % Allowed : 17.79 % Favored : 79.95 % 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: 5.00 (0.40), residues: 516 helix: 4.57 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.39 (0.60), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.003 0.001 HIS A 64 PHE 0.009 0.001 PHE U 262 TYR 0.021 0.001 TYR U 155 ARG 0.001 0.000 ARG A 56 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8713 (OUTLIER) cc_final: 0.8486 (tt0) REVERT: U 158 LYS cc_start: 0.9011 (tmmt) cc_final: 0.8555 (tppp) REVERT: U 191 LYS cc_start: 0.9509 (mttt) cc_final: 0.9038 (pttt) REVERT: A 46 GLU cc_start: 0.8783 (OUTLIER) cc_final: 0.8466 (tt0) REVERT: A 90 ASN cc_start: 0.8860 (m110) cc_final: 0.8503 (p0) REVERT: A 191 LYS cc_start: 0.9526 (mmtt) cc_final: 0.8860 (tttt) outliers start: 10 outliers final: 6 residues processed: 65 average time/residue: 1.7106 time to fit residues: 115.4423 Evaluate side-chains 64 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 1.255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 15 optimal weight: 8.9990 chunk 11 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 34 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 18 optimal weight: 0.1980 chunk 30 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 21 optimal weight: 0.0040 overall best weight: 0.5192 ------------------------------------------------------------------------------- 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 = 0.3353 r_free = 0.3353 target = 0.094705 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3022 r_free = 0.3022 target = 0.075843 restraints weight = 10095.905| |-----------------------------------------------------------------------------| r_work (start): 0.2998 rms_B_bonded: 3.08 r_work: 0.2869 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8107 moved from start: 0.2845 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4578 Z= 0.179 Angle : 0.525 6.628 6072 Z= 0.277 Chirality : 0.032 0.101 646 Planarity : 0.002 0.022 730 Dihedral : 7.365 59.598 780 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 2.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.58 % Allowed : 18.92 % Favored : 79.50 % 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: 5.08 (0.40), residues: 516 helix: 4.60 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.25 (0.61), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 95 HIS 0.003 0.000 HIS A 64 PHE 0.007 0.001 PHE U 262 TYR 0.018 0.001 TYR U 155 ARG 0.001 0.000 ARG A 163 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 64 time to evaluate : 0.455 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8730 (OUTLIER) cc_final: 0.8491 (tt0) REVERT: U 158 LYS cc_start: 0.8966 (tmmt) cc_final: 0.8372 (tppp) REVERT: U 190 TRP cc_start: 0.8629 (m100) cc_final: 0.7898 (m-10) REVERT: U 191 LYS cc_start: 0.9523 (mttt) cc_final: 0.9079 (pttt) REVERT: U 213 SER cc_start: 0.8711 (m) cc_final: 0.8051 (t) REVERT: A 46 GLU cc_start: 0.8812 (OUTLIER) cc_final: 0.8469 (tt0) REVERT: A 90 ASN cc_start: 0.8938 (m110) cc_final: 0.8600 (p0) REVERT: A 191 LYS cc_start: 0.9531 (mmtt) cc_final: 0.8878 (tttt) outliers start: 7 outliers final: 6 residues processed: 71 average time/residue: 0.9393 time to fit residues: 70.1251 Evaluate side-chains 62 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 54 time to evaluate : 0.517 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 6 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 44 optimal weight: 0.0020 chunk 10 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 41 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 overall best weight: 0.6788 ------------------------------------------------------------------------------- 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 = 0.3324 r_free = 0.3324 target = 0.092994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.074164 restraints weight = 10170.037| |-----------------------------------------------------------------------------| r_work (start): 0.2963 rms_B_bonded: 3.07 r_work: 0.2832 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2832 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.2847 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4578 Z= 0.193 Angle : 0.551 7.187 6072 Z= 0.291 Chirality : 0.032 0.100 646 Planarity : 0.002 0.019 730 Dihedral : 7.301 59.767 780 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 1.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.01 % Favored : 93.99 % Rotamer: Outliers : 1.80 % Allowed : 19.82 % Favored : 78.38 % 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: 5.11 (0.40), residues: 516 helix: 4.62 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.25 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.003 0.000 HIS A 64 PHE 0.008 0.001 PHE U 262 TYR 0.007 0.001 TYR U 30 ARG 0.001 0.000 ARG A 68 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 60 time to evaluate : 0.562 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8743 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: U 158 LYS cc_start: 0.9001 (tmmt) cc_final: 0.8404 (tppp) REVERT: U 190 TRP cc_start: 0.8670 (m100) cc_final: 0.7935 (m-10) REVERT: U 191 LYS cc_start: 0.9523 (mttt) cc_final: 0.9082 (pttt) REVERT: U 213 SER cc_start: 0.8872 (m) cc_final: 0.8218 (t) REVERT: A 46 GLU cc_start: 0.8787 (OUTLIER) cc_final: 0.8451 (tt0) REVERT: A 90 ASN cc_start: 0.8941 (m110) cc_final: 0.8644 (p0) REVERT: A 191 LYS cc_start: 0.9539 (mmtt) cc_final: 0.8870 (tttt) outliers start: 8 outliers final: 6 residues processed: 67 average time/residue: 1.3705 time to fit residues: 95.7820 Evaluate side-chains 60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.503 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 21 optimal weight: 0.0770 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 29 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 overall best weight: 0.6538 ------------------------------------------------------------------------------- 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 = 0.3332 r_free = 0.3332 target = 0.093518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2999 r_free = 0.2999 target = 0.074676 restraints weight = 10044.959| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 3.06 r_work: 0.2839 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2839 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.2865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4578 Z= 0.195 Angle : 0.562 7.749 6072 Z= 0.296 Chirality : 0.032 0.101 646 Planarity : 0.002 0.021 730 Dihedral : 7.145 58.614 780 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 1.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 2.25 % Allowed : 19.37 % Favored : 78.38 % 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: 5.11 (0.40), residues: 516 helix: 4.61 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.20 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.003 0.000 HIS A 64 PHE 0.008 0.001 PHE U 262 TYR 0.019 0.001 TYR U 155 ARG 0.001 0.000 ARG A 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 65 time to evaluate : 0.864 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8748 (OUTLIER) cc_final: 0.8521 (tt0) REVERT: U 158 LYS cc_start: 0.8991 (tmmt) cc_final: 0.8423 (tppp) REVERT: U 190 TRP cc_start: 0.8689 (m100) cc_final: 0.7844 (m-10) REVERT: U 191 LYS cc_start: 0.9519 (mttt) cc_final: 0.9071 (pttt) REVERT: A 46 GLU cc_start: 0.8791 (OUTLIER) cc_final: 0.8518 (tt0) REVERT: A 90 ASN cc_start: 0.8969 (m110) cc_final: 0.8650 (p0) REVERT: A 191 LYS cc_start: 0.9546 (mmtt) cc_final: 0.8860 (tttt) outliers start: 10 outliers final: 7 residues processed: 74 average time/residue: 1.2088 time to fit residues: 94.0296 Evaluate side-chains 61 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 273 TYR Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 9 optimal weight: 0.7980 chunk 36 optimal weight: 0.2980 chunk 46 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 33 optimal weight: 4.9990 chunk 45 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 48 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 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 = 0.3339 r_free = 0.3339 target = 0.094469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.075255 restraints weight = 9878.761| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 3.10 r_work: 0.2840 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 4578 Z= 0.202 Angle : 0.578 8.148 6072 Z= 0.305 Chirality : 0.032 0.100 646 Planarity : 0.002 0.020 730 Dihedral : 7.078 57.766 780 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 2.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 2.03 % Allowed : 20.27 % Favored : 77.70 % 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: 5.08 (0.40), residues: 516 helix: 4.60 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.25 (0.62), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 95 HIS 0.003 0.000 HIS A 64 PHE 0.008 0.001 PHE U 262 TYR 0.005 0.001 TYR A 78 ARG 0.001 0.000 ARG U 56 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 51 time to evaluate : 0.678 Fit side-chains revert: symmetry clash REVERT: U 46 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.8442 (tt0) REVERT: U 158 LYS cc_start: 0.8950 (tmmt) cc_final: 0.8391 (tppp) REVERT: U 190 TRP cc_start: 0.8674 (m100) cc_final: 0.7862 (m-10) REVERT: U 191 LYS cc_start: 0.9514 (mttt) cc_final: 0.9037 (pttt) REVERT: A 46 GLU cc_start: 0.8726 (OUTLIER) cc_final: 0.8467 (tt0) REVERT: A 90 ASN cc_start: 0.8938 (m110) cc_final: 0.8634 (p0) REVERT: A 191 LYS cc_start: 0.9537 (mmtt) cc_final: 0.8832 (tttt) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 1.2563 time to fit residues: 77.7789 Evaluate side-chains 59 residues out of total 444 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 1.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 46 GLU Chi-restraints excluded: chain U residue 156 ILE Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 280 SER Chi-restraints excluded: chain A residue 20 PHE Chi-restraints excluded: chain A residue 46 GLU Chi-restraints excluded: chain A residue 207 LEU Chi-restraints excluded: chain A residue 280 SER Chi-restraints excluded: chain A residue 286 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 37 optimal weight: 0.8980 chunk 41 optimal weight: 0.0370 chunk 42 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 45 optimal weight: 0.7980 chunk 19 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5658 ------------------------------------------------------------------------------- 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 = 0.3344 r_free = 0.3344 target = 0.094356 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3012 r_free = 0.3012 target = 0.075604 restraints weight = 10070.859| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 3.05 r_work: 0.2867 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8131 moved from start: 0.3084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 4578 Z= 0.194 Angle : 0.570 8.178 6072 Z= 0.300 Chirality : 0.032 0.101 646 Planarity : 0.002 0.020 730 Dihedral : 6.880 57.373 780 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 1.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 1.80 % Allowed : 20.50 % Favored : 77.70 % 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: 5.09 (0.40), residues: 516 helix: 4.60 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -2.25 (0.63), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 95 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE U 262 TYR 0.006 0.001 TYR A 30 ARG 0.001 0.000 ARG A 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3757.44 seconds wall clock time: 68 minutes 45.39 seconds (4125.39 seconds total)