Starting phenix.real_space_refine on Thu Mar 6 03:13:38 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bws_44978/03_2025/9bws_44978_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bws_44978/03_2025/9bws_44978.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.39 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bws_44978/03_2025/9bws_44978.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bws_44978/03_2025/9bws_44978.map" model { file = "/net/cci-nas-00/data/ceres_data/9bws_44978/03_2025/9bws_44978_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bws_44978/03_2025/9bws_44978_trim.cif" } resolution = 2.39 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= 0.014 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 4 8.98 5 S 28 5.16 5 C 2868 2.51 5 N 678 2.21 5 O 708 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4286 Number of models: 1 Model: "" Number of chains: 4 Chain: "U" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2051 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Chain: "A" Number of atoms: 2051 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2051 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 5, 'TRANS': 251} Chain breaks: 1 Chain: "U" Number of atoms: 91 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 91 Unusual residues: {' K': 1, 'D10': 2, 'D12': 1, 'EIC': 1, 'HEX': 1, 'OCT': 4} Classifications: {'undetermined': 10} Link IDs: {None: 9} Chain: "A" Number of atoms: 93 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 93 Unusual residues: {' K': 3, 'D10': 2, 'D12': 1, 'EIC': 1, 'HEX': 1, 'OCT': 4} Classifications: {'undetermined': 12} Link IDs: {None: 11} Time building chain proxies: 4.19, per 1000 atoms: 0.98 Number of scatterers: 4286 At special positions: 0 Unit cell: (68.47, 74.315, 94.355, 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 4 19.00 S 28 16.00 O 708 8.00 N 678 7.00 C 2868 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: 2.38 Conformation dependent library (CDL) restraints added in 473.0 milliseconds 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 952 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 78.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'U' and resid 14 through 65 removed outlier: 5.540A pdb=" N ALA U 44 " --> pdb=" O ALA U 40 " (cutoff:3.500A) removed outlier: 5.433A pdb=" N HIS U 45 " --> pdb=" O LEU U 41 " (cutoff:3.500A) Processing helix chain 'U' and resid 67 through 83 Processing helix chain 'U' and resid 97 through 109 Processing helix chain 'U' and resid 124 through 162 Proline residue: U 136 - end of helix Processing helix chain 'U' and resid 193 through 215 removed outlier: 3.912A 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 294 removed outlier: 3.759A pdb=" N PHE U 259 " --> pdb=" O GLY U 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 15 through 64 removed outlier: 5.555A pdb=" N ALA A 44 " --> pdb=" O ALA A 40 " (cutoff:3.500A) removed outlier: 5.314A pdb=" N HIS A 45 " --> pdb=" O LEU A 41 " (cutoff:3.500A) Processing helix chain 'A' and resid 67 through 85 removed outlier: 3.589A pdb=" N GLU A 80 " --> pdb=" O ARG A 76 " (cutoff:3.500A) removed outlier: 3.537A pdb=" N ALA A 81 " --> pdb=" O HIS A 77 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N ALA A 84 " --> pdb=" O GLU A 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 109 Processing helix chain 'A' and resid 122 through 162 Proline residue: A 136 - end of helix Processing helix chain 'A' and resid 193 through 220 removed outlier: 3.582A pdb=" N MET A 215 " --> pdb=" O CYS A 211 " (cutoff:3.500A) Proline residue: A 218 - end of helix Processing helix chain 'A' and resid 223 through 236 Processing helix chain 'A' and resid 255 through 294 removed outlier: 3.869A pdb=" N PHE A 259 " --> pdb=" O GLY A 255 " (cutoff:3.500A) 328 hydrogen bonds defined for protein. 984 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: 1.05 Time building geometry restraints manager: 1.62 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 723 1.33 - 1.45: 1183 1.45 - 1.57: 2422 1.57 - 1.69: 0 1.69 - 1.81: 40 Bond restraints: 4368 Sorted by residual: bond pdb=" N ILE A 86 " pdb=" CA ILE A 86 " ideal model delta sigma weight residual 1.459 1.493 -0.034 1.17e-02 7.31e+03 8.63e+00 bond pdb=" N TYR U 216 " pdb=" CA TYR U 216 " ideal model delta sigma weight residual 1.457 1.493 -0.035 1.29e-02 6.01e+03 7.55e+00 bond pdb=" N SER A 67 " pdb=" CA SER A 67 " ideal model delta sigma weight residual 1.454 1.486 -0.032 1.18e-02 7.18e+03 7.30e+00 bond pdb=" CA ALA A 84 " pdb=" CB ALA A 84 " ideal model delta sigma weight residual 1.529 1.482 0.047 1.74e-02 3.30e+03 7.20e+00 bond pdb=" N GLU A 79 " pdb=" CA GLU A 79 " ideal model delta sigma weight residual 1.459 1.490 -0.031 1.21e-02 6.83e+03 6.46e+00 ... (remaining 4363 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.39: 5559 1.39 - 2.78: 206 2.78 - 4.17: 54 4.17 - 5.56: 18 5.56 - 6.95: 3 Bond angle restraints: 5840 Sorted by residual: angle pdb=" N ALA A 84 " pdb=" CA ALA A 84 " pdb=" C ALA A 84 " ideal model delta sigma weight residual 112.54 107.85 4.69 1.22e+00 6.72e-01 1.48e+01 angle pdb=" N GLU A 80 " pdb=" CA GLU A 80 " pdb=" CB GLU A 80 " ideal model delta sigma weight residual 110.22 104.77 5.45 1.54e+00 4.22e-01 1.25e+01 angle pdb=" CA TYR U 216 " pdb=" CB TYR U 216 " pdb=" CG TYR U 216 " ideal model delta sigma weight residual 113.90 119.91 -6.01 1.80e+00 3.09e-01 1.11e+01 angle pdb=" N GLU U 220 " pdb=" CA GLU U 220 " pdb=" C GLU U 220 " ideal model delta sigma weight residual 109.54 114.03 -4.49 1.37e+00 5.33e-01 1.07e+01 angle pdb=" N GLY U 221 " pdb=" CA GLY U 221 " pdb=" C GLY U 221 " ideal model delta sigma weight residual 113.18 120.13 -6.95 2.37e+00 1.78e-01 8.61e+00 ... (remaining 5835 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.78: 2234 17.78 - 35.56: 240 35.56 - 53.34: 47 53.34 - 71.12: 12 71.12 - 88.91: 1 Dihedral angle restraints: 2534 sinusoidal: 1048 harmonic: 1486 Sorted by residual: dihedral pdb=" CA ASP U 96 " pdb=" C ASP U 96 " pdb=" N PHE U 97 " pdb=" CA PHE U 97 " ideal model delta harmonic sigma weight residual 180.00 152.29 27.71 0 5.00e+00 4.00e-02 3.07e+01 dihedral pdb=" CA ASP A 89 " pdb=" C ASP A 89 " pdb=" N ASN A 90 " pdb=" CA ASN A 90 " ideal model delta harmonic sigma weight residual 180.00 154.96 25.04 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA TRP A 95 " pdb=" C TRP A 95 " pdb=" N ASP A 96 " pdb=" CA ASP A 96 " ideal model delta harmonic sigma weight residual 180.00 157.41 22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 2531 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 444 0.030 - 0.059: 119 0.059 - 0.089: 47 0.089 - 0.119: 20 0.119 - 0.148: 4 Chirality restraints: 634 Sorted by residual: chirality pdb=" CA TYR U 216 " pdb=" N TYR U 216 " pdb=" C TYR U 216 " pdb=" CB TYR U 216 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA ILE A 86 " pdb=" N ILE A 86 " pdb=" C ILE A 86 " pdb=" CB ILE A 86 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.14e-01 chirality pdb=" CA ALA A 84 " pdb=" N ALA A 84 " pdb=" C ALA A 84 " pdb=" CB ALA A 84 " both_signs ideal model delta sigma weight residual False 2.48 2.62 -0.13 2.00e-01 2.50e+01 4.49e-01 ... (remaining 631 not shown) Planarity restraints: 712 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG A 83 " -0.283 9.50e-02 1.11e+02 1.27e-01 9.89e+00 pdb=" NE ARG A 83 " 0.016 2.00e-02 2.50e+03 pdb=" CZ ARG A 83 " 0.005 2.00e-02 2.50e+03 pdb=" NH1 ARG A 83 " 0.002 2.00e-02 2.50e+03 pdb=" NH2 ARG A 83 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 210 " 0.012 2.00e-02 2.50e+03 2.43e-02 5.90e+00 pdb=" C CYS A 210 " -0.042 2.00e-02 2.50e+03 pdb=" O CYS A 210 " 0.016 2.00e-02 2.50e+03 pdb=" N CYS A 211 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG U 292 " 0.177 9.50e-02 1.11e+02 7.99e-02 5.22e+00 pdb=" NE ARG U 292 " -0.017 2.00e-02 2.50e+03 pdb=" CZ ARG U 292 " 0.018 2.00e-02 2.50e+03 pdb=" NH1 ARG U 292 " -0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG U 292 " -0.000 2.00e-02 2.50e+03 ... (remaining 709 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.86: 1490 2.86 - 3.43: 4608 3.43 - 4.00: 7451 4.00 - 4.57: 10948 4.57 - 5.14: 15350 Nonbonded interactions: 39847 Sorted by model distance: nonbonded pdb=" O GLU A 79 " pdb=" OG1 THR A 82 " model vdw 2.288 3.040 nonbonded pdb=" O SER A 236 " pdb=" OG1 THR A 237 " model vdw 2.345 3.040 nonbonded pdb=" O SER U 236 " pdb=" OG1 THR U 237 " model vdw 2.385 3.040 nonbonded pdb=" N ASP U 96 " pdb=" OD1 ASP U 96 " model vdw 2.402 3.120 nonbonded pdb=" OE1 GLU U 46 " pdb=" O ARG A 94 " model vdw 2.411 3.040 ... (remaining 39842 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 404 or resid 410)) selection = (chain 'U' and (resid 14 through 295 or resid 404 or resid 410)) } 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: 1.710 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: 0.220 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.900 Find NCS groups from input model: 0.190 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:14.190 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 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 : 0.004 0.047 4368 Z= 0.257 Angle : 0.677 6.953 5840 Z= 0.376 Chirality : 0.036 0.148 634 Planarity : 0.008 0.127 712 Dihedral : 14.795 88.905 1582 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 0.93 % Allowed : 11.34 % Favored : 87.73 % 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: 4.00 (0.39), residues: 506 helix: 3.87 (0.25), residues: 390 sheet: None (None), residues: 0 loop : -2.17 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP U 53 HIS 0.004 0.001 HIS U 77 PHE 0.010 0.002 PHE A 232 TYR 0.009 0.001 TYR U 216 ARG 0.020 0.001 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 110 time to evaluate : 0.455 Fit side-chains REVERT: U 251 TYR cc_start: 0.7937 (OUTLIER) cc_final: 0.6626 (t80) REVERT: A 251 TYR cc_start: 0.7624 (OUTLIER) cc_final: 0.6083 (t80) outliers start: 4 outliers final: 2 residues processed: 113 average time/residue: 1.3617 time to fit residues: 158.3624 Evaluate side-chains 80 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 67 SER Chi-restraints excluded: chain A residue 242 ASP Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 0.9980 chunk 37 optimal weight: 0.7980 chunk 21 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 4.9990 chunk 15 optimal weight: 0.0270 chunk 23 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6638 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 48 GLN A 48 GLN A 65 GLN A 288 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.099744 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.077784 restraints weight = 7288.675| |-----------------------------------------------------------------------------| r_work (start): 0.2961 rms_B_bonded: 2.41 r_work: 0.2829 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2723 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4368 Z= 0.190 Angle : 0.531 5.178 5840 Z= 0.289 Chirality : 0.034 0.172 634 Planarity : 0.003 0.024 712 Dihedral : 9.670 58.817 691 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 3.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 2.31 % Allowed : 15.74 % Favored : 81.94 % 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: 4.53 (0.38), residues: 506 helix: 3.76 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.73 (0.70), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP U 95 HIS 0.004 0.001 HIS U 64 PHE 0.009 0.001 PHE U 232 TYR 0.018 0.001 TYR U 195 ARG 0.004 0.001 ARG U 148 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.507 Fit side-chains REVERT: U 54 GLU cc_start: 0.8776 (tp30) cc_final: 0.8467 (tp30) REVERT: U 220 GLU cc_start: 0.8320 (pt0) cc_final: 0.7964 (pt0) REVERT: U 251 TYR cc_start: 0.8442 (OUTLIER) cc_final: 0.6954 (t80) REVERT: A 54 GLU cc_start: 0.8808 (tp30) cc_final: 0.8557 (tp30) REVERT: A 62 ARG cc_start: 0.8550 (ttp-110) cc_final: 0.8281 (ttp-110) REVERT: A 251 TYR cc_start: 0.8494 (OUTLIER) cc_final: 0.6673 (t80) outliers start: 10 outliers final: 2 residues processed: 96 average time/residue: 1.5933 time to fit residues: 158.0555 Evaluate side-chains 84 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 153 ILE Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 33 optimal weight: 0.0870 chunk 49 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 3.9990 chunk 13 optimal weight: 0.6980 overall best weight: 0.5758 ------------------------------------------------------------------------------- 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 = 0.3297 r_free = 0.3297 target = 0.098739 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.076642 restraints weight = 7163.599| |-----------------------------------------------------------------------------| r_work (start): 0.2933 rms_B_bonded: 2.38 r_work: 0.2802 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2694 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.3926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4368 Z= 0.174 Angle : 0.527 7.494 5840 Z= 0.274 Chirality : 0.033 0.180 634 Planarity : 0.003 0.026 712 Dihedral : 8.424 56.246 688 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 1.62 % Allowed : 15.97 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.82 (0.38), residues: 506 helix: 3.94 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.52 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP U 95 HIS 0.003 0.000 HIS U 64 PHE 0.006 0.001 PHE A 232 TYR 0.007 0.001 TYR U 78 ARG 0.006 0.000 ARG A 87 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.530 Fit side-chains REVERT: U 51 GLN cc_start: 0.8805 (tp40) cc_final: 0.8581 (tm-30) REVERT: U 54 GLU cc_start: 0.8773 (tp30) cc_final: 0.8484 (tp30) REVERT: U 220 GLU cc_start: 0.8254 (pt0) cc_final: 0.7940 (pt0) REVERT: U 251 TYR cc_start: 0.8414 (OUTLIER) cc_final: 0.6948 (t80) REVERT: A 51 GLN cc_start: 0.8813 (tp40) cc_final: 0.8592 (tm-30) REVERT: A 54 GLU cc_start: 0.8726 (tp30) cc_final: 0.8442 (tp30) REVERT: A 251 TYR cc_start: 0.8396 (OUTLIER) cc_final: 0.8131 (m-80) outliers start: 7 outliers final: 2 residues processed: 83 average time/residue: 1.7538 time to fit residues: 149.5051 Evaluate side-chains 80 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 76 time to evaluate : 0.494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 207 LEU Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 4.9990 chunk 22 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 35 optimal weight: 4.9990 chunk 11 optimal weight: 0.6980 chunk 47 optimal weight: 0.5980 chunk 37 optimal weight: 0.8980 chunk 19 optimal weight: 0.6980 chunk 44 optimal weight: 0.8980 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.096954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.075015 restraints weight = 7281.137| |-----------------------------------------------------------------------------| r_work (start): 0.2903 rms_B_bonded: 2.38 r_work: 0.2766 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4368 Z= 0.190 Angle : 0.539 6.605 5840 Z= 0.284 Chirality : 0.034 0.182 634 Planarity : 0.003 0.023 712 Dihedral : 8.305 58.913 688 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 1.62 % Allowed : 14.81 % Favored : 83.56 % 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: 4.83 (0.38), residues: 506 helix: 3.96 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.61 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 PHE 0.008 0.001 PHE A 97 TYR 0.014 0.001 TYR U 195 ARG 0.007 0.001 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.490 Fit side-chains REVERT: U 51 GLN cc_start: 0.8807 (tp40) cc_final: 0.8550 (tm-30) REVERT: U 54 GLU cc_start: 0.8765 (tp30) cc_final: 0.8517 (tp30) REVERT: U 251 TYR cc_start: 0.8518 (OUTLIER) cc_final: 0.6944 (t80) REVERT: U 292 ARG cc_start: 0.8975 (ttm-80) cc_final: 0.8623 (ttm110) REVERT: A 51 GLN cc_start: 0.8788 (tp40) cc_final: 0.8527 (tm-30) REVERT: A 54 GLU cc_start: 0.8711 (tp30) cc_final: 0.8329 (tp30) REVERT: A 251 TYR cc_start: 0.8551 (OUTLIER) cc_final: 0.8277 (m-80) REVERT: A 292 ARG cc_start: 0.8942 (ttm-80) cc_final: 0.8646 (ttm110) outliers start: 7 outliers final: 1 residues processed: 78 average time/residue: 1.6976 time to fit residues: 135.9494 Evaluate side-chains 70 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 67 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 251 TYR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 37 optimal weight: 0.9980 chunk 43 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 9 optimal weight: 0.7980 chunk 6 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 = 0.3272 r_free = 0.3272 target = 0.095595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2899 r_free = 0.2899 target = 0.073230 restraints weight = 7424.794| |-----------------------------------------------------------------------------| r_work (start): 0.2889 rms_B_bonded: 2.41 r_work: 0.2755 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2648 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4368 Z= 0.211 Angle : 0.544 7.087 5840 Z= 0.287 Chirality : 0.034 0.190 634 Planarity : 0.003 0.022 712 Dihedral : 8.413 59.208 688 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 1.16 % Allowed : 14.81 % Favored : 84.03 % 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: 4.74 (0.38), residues: 506 helix: 3.92 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.76 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 PHE 0.008 0.001 PHE A 97 TYR 0.012 0.001 TYR U 195 ARG 0.004 0.000 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.451 Fit side-chains REVERT: U 51 GLN cc_start: 0.8818 (tp40) cc_final: 0.8550 (tm-30) REVERT: U 54 GLU cc_start: 0.8791 (tp30) cc_final: 0.8471 (tp30) REVERT: U 251 TYR cc_start: 0.8586 (OUTLIER) cc_final: 0.6989 (t80) REVERT: U 292 ARG cc_start: 0.8941 (ttm-80) cc_final: 0.8597 (ttm110) REVERT: A 51 GLN cc_start: 0.8833 (tp40) cc_final: 0.8554 (tm-30) REVERT: A 54 GLU cc_start: 0.8711 (tp30) cc_final: 0.8260 (tp30) REVERT: A 292 ARG cc_start: 0.8903 (ttm-80) cc_final: 0.8605 (ttm110) outliers start: 5 outliers final: 2 residues processed: 73 average time/residue: 1.8182 time to fit residues: 136.1014 Evaluate side-chains 75 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.496 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.1980 chunk 4 optimal weight: 0.9990 chunk 44 optimal weight: 0.7980 chunk 13 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 chunk 6 optimal weight: 0.0070 overall best weight: 0.4998 ------------------------------------------------------------------------------- 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 = 0.3311 r_free = 0.3311 target = 0.098628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.076156 restraints weight = 7295.332| |-----------------------------------------------------------------------------| r_work (start): 0.2935 rms_B_bonded: 2.41 r_work: 0.2801 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2692 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4368 Z= 0.174 Angle : 0.526 5.389 5840 Z= 0.278 Chirality : 0.033 0.193 634 Planarity : 0.003 0.021 712 Dihedral : 7.496 55.749 686 Min Nonbonded Distance : 2.584 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.93 % Allowed : 16.44 % Favored : 82.64 % 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: 4.85 (0.38), residues: 506 helix: 4.02 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.80 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 95 HIS 0.002 0.000 HIS A 64 PHE 0.007 0.001 PHE A 97 TYR 0.012 0.001 TYR U 195 ARG 0.004 0.000 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 80 time to evaluate : 0.497 Fit side-chains REVERT: U 51 GLN cc_start: 0.8805 (tp40) cc_final: 0.8516 (tm-30) REVERT: U 54 GLU cc_start: 0.8779 (tp30) cc_final: 0.8455 (tp30) REVERT: U 190 TRP cc_start: 0.7998 (m100) cc_final: 0.7697 (m-10) REVERT: U 251 TYR cc_start: 0.8558 (OUTLIER) cc_final: 0.6909 (t80) REVERT: U 292 ARG cc_start: 0.8918 (ttm-80) cc_final: 0.8601 (ttm110) REVERT: A 51 GLN cc_start: 0.8789 (tp40) cc_final: 0.8516 (tm-30) REVERT: A 54 GLU cc_start: 0.8692 (tp30) cc_final: 0.8258 (tp30) REVERT: A 292 ARG cc_start: 0.8876 (ttm-80) cc_final: 0.8571 (ttm110) outliers start: 4 outliers final: 2 residues processed: 81 average time/residue: 1.7739 time to fit residues: 147.3579 Evaluate side-chains 78 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 251 TYR Chi-restraints excluded: chain A residue 156 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 10 optimal weight: 0.0770 chunk 14 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 17 optimal weight: 0.2980 chunk 43 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.097925 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2937 r_free = 0.2937 target = 0.075369 restraints weight = 7342.047| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.41 r_work: 0.2792 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2683 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2683 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8340 moved from start: 0.4453 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4368 Z= 0.185 Angle : 0.547 6.342 5840 Z= 0.289 Chirality : 0.033 0.198 634 Planarity : 0.003 0.021 712 Dihedral : 7.190 54.353 686 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.69 % Allowed : 16.90 % Favored : 82.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.85 (0.38), residues: 506 helix: 4.02 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.83 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 PHE 0.006 0.001 PHE U 232 TYR 0.013 0.001 TYR U 195 ARG 0.004 0.000 ARG A 62 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 75 time to evaluate : 0.454 Fit side-chains REVERT: U 51 GLN cc_start: 0.8810 (tp40) cc_final: 0.8517 (tm-30) REVERT: U 54 GLU cc_start: 0.8774 (tp30) cc_final: 0.8326 (tp30) REVERT: U 190 TRP cc_start: 0.8017 (m100) cc_final: 0.7711 (m-10) REVERT: U 251 TYR cc_start: 0.8581 (OUTLIER) cc_final: 0.6900 (t80) REVERT: U 292 ARG cc_start: 0.8919 (ttm-80) cc_final: 0.8604 (ttm110) REVERT: A 51 GLN cc_start: 0.8788 (tp40) cc_final: 0.8499 (tm-30) REVERT: A 54 GLU cc_start: 0.8679 (tp30) cc_final: 0.8246 (tp30) REVERT: A 65 GLN cc_start: 0.8706 (pm20) cc_final: 0.8250 (mp10) REVERT: A 292 ARG cc_start: 0.8872 (ttm-80) cc_final: 0.8576 (ttm110) outliers start: 3 outliers final: 2 residues processed: 76 average time/residue: 1.5866 time to fit residues: 123.8377 Evaluate side-chains 77 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 74 time to evaluate : 0.501 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 14 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 11 optimal weight: 0.7980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.5980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.096064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2903 r_free = 0.2903 target = 0.073522 restraints weight = 7227.031| |-----------------------------------------------------------------------------| r_work (start): 0.2900 rms_B_bonded: 2.40 r_work: 0.2766 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2656 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.4553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4368 Z= 0.210 Angle : 0.562 6.541 5840 Z= 0.298 Chirality : 0.034 0.195 634 Planarity : 0.003 0.021 712 Dihedral : 7.336 54.004 686 Min Nonbonded Distance : 2.613 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer: Outliers : 0.93 % Allowed : 17.82 % Favored : 81.25 % 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: 4.80 (0.38), residues: 506 helix: 3.98 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.81 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.002 0.000 HIS A 64 PHE 0.010 0.001 PHE A 97 TYR 0.012 0.001 TYR U 195 ARG 0.003 0.000 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.450 Fit side-chains REVERT: U 51 GLN cc_start: 0.8834 (tp40) cc_final: 0.8532 (tm-30) REVERT: U 54 GLU cc_start: 0.8788 (tp30) cc_final: 0.8356 (tp30) REVERT: U 65 GLN cc_start: 0.8759 (pm20) cc_final: 0.8499 (mp10) REVERT: U 190 TRP cc_start: 0.8047 (m100) cc_final: 0.7746 (m-10) REVERT: U 251 TYR cc_start: 0.8612 (OUTLIER) cc_final: 0.6938 (t80) REVERT: U 292 ARG cc_start: 0.8939 (ttm-80) cc_final: 0.8617 (ttm110) REVERT: A 51 GLN cc_start: 0.8812 (tp40) cc_final: 0.8506 (tm-30) REVERT: A 54 GLU cc_start: 0.8689 (tp30) cc_final: 0.8269 (tp30) REVERT: A 292 ARG cc_start: 0.8911 (ttm-80) cc_final: 0.8604 (ttm110) outliers start: 4 outliers final: 2 residues processed: 73 average time/residue: 1.6105 time to fit residues: 120.8096 Evaluate side-chains 75 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 chunk 39 optimal weight: 0.0470 chunk 26 optimal weight: 2.9990 chunk 47 optimal weight: 0.5980 chunk 22 optimal weight: 0.6980 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 36 optimal weight: 0.6980 overall best weight: 0.5478 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.098246 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.2931 r_free = 0.2931 target = 0.075628 restraints weight = 7323.488| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.42 r_work: 0.2788 rms_B_bonded: 2.92 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.73 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.4579 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4368 Z= 0.194 Angle : 0.581 7.990 5840 Z= 0.306 Chirality : 0.034 0.201 634 Planarity : 0.003 0.023 712 Dihedral : 7.031 51.513 686 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 2.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.69 % Allowed : 17.82 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 4.84 (0.38), residues: 506 helix: 4.01 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.80 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 95 HIS 0.004 0.001 HIS A 64 PHE 0.006 0.001 PHE A 97 TYR 0.007 0.001 TYR U 78 ARG 0.003 0.000 ARG U 292 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 72 time to evaluate : 0.452 Fit side-chains REVERT: U 51 GLN cc_start: 0.8832 (tp40) cc_final: 0.8538 (tm-30) REVERT: U 54 GLU cc_start: 0.8785 (tp30) cc_final: 0.8347 (tp30) REVERT: U 190 TRP cc_start: 0.8065 (m100) cc_final: 0.7773 (m-10) REVERT: U 251 TYR cc_start: 0.8622 (OUTLIER) cc_final: 0.6927 (t80) REVERT: U 292 ARG cc_start: 0.8909 (ttm-80) cc_final: 0.8585 (ttm110) REVERT: A 51 GLN cc_start: 0.8798 (tp40) cc_final: 0.8497 (tm-30) REVERT: A 54 GLU cc_start: 0.8678 (tp30) cc_final: 0.8263 (tp30) REVERT: A 65 GLN cc_start: 0.8687 (pm20) cc_final: 0.8336 (mp10) REVERT: A 292 ARG cc_start: 0.8887 (ttm-80) cc_final: 0.8584 (ttm110) outliers start: 3 outliers final: 1 residues processed: 73 average time/residue: 1.6410 time to fit residues: 123.0375 Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 74 time to evaluate : 0.515 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 13 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 41 optimal weight: 0.8980 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 3.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 1.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.096156 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2901 r_free = 0.2901 target = 0.073668 restraints weight = 7153.458| |-----------------------------------------------------------------------------| r_work (start): 0.2888 rms_B_bonded: 2.39 r_work: 0.2755 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2646 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2646 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.4621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4368 Z= 0.224 Angle : 0.597 8.360 5840 Z= 0.317 Chirality : 0.035 0.197 634 Planarity : 0.003 0.025 712 Dihedral : 7.323 48.708 686 Min Nonbonded Distance : 2.599 Molprobity Statistics. All-atom Clashscore : 2.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 0.69 % Allowed : 18.06 % Favored : 81.25 % 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: 4.81 (0.38), residues: 506 helix: 3.98 (0.24), residues: 408 sheet: None (None), residues: 0 loop : -0.81 (0.72), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP U 53 HIS 0.002 0.001 HIS A 64 PHE 0.009 0.001 PHE A 97 TYR 0.010 0.001 TYR U 195 ARG 0.003 0.000 ARG U 292 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1012 Ramachandran restraints generated. 506 Oldfield, 0 Emsley, 506 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.499 Fit side-chains REVERT: U 51 GLN cc_start: 0.8845 (tp40) cc_final: 0.8538 (tm-30) REVERT: U 54 GLU cc_start: 0.8769 (tp30) cc_final: 0.8348 (tp30) REVERT: U 190 TRP cc_start: 0.8064 (m100) cc_final: 0.7766 (m-10) REVERT: U 251 TYR cc_start: 0.8638 (OUTLIER) cc_final: 0.6953 (t80) REVERT: U 292 ARG cc_start: 0.8902 (ttm-80) cc_final: 0.8594 (ttm110) REVERT: A 51 GLN cc_start: 0.8828 (tp40) cc_final: 0.8528 (tm-30) REVERT: A 54 GLU cc_start: 0.8675 (tp30) cc_final: 0.8264 (tp30) REVERT: A 292 ARG cc_start: 0.8874 (ttm-80) cc_final: 0.8592 (ttm110) outliers start: 3 outliers final: 2 residues processed: 74 average time/residue: 1.6590 time to fit residues: 126.1292 Evaluate side-chains 76 residues out of total 432 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 73 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain U residue 220 GLU Chi-restraints excluded: chain U residue 247 GLN Chi-restraints excluded: chain U residue 251 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 38 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 10 optimal weight: 0.0670 chunk 19 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 11 optimal weight: 0.0470 chunk 3 optimal weight: 0.9980 chunk 36 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.5016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: U 90 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.098489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2933 r_free = 0.2933 target = 0.075705 restraints weight = 7265.965| |-----------------------------------------------------------------------------| r_work (start): 0.2923 rms_B_bonded: 2.43 r_work: 0.2788 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2677 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8366 moved from start: 0.4631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4368 Z= 0.192 Angle : 0.603 8.798 5840 Z= 0.319 Chirality : 0.034 0.203 634 Planarity : 0.003 0.026 712 Dihedral : 6.910 48.484 686 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 2.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.35 % Favored : 95.65 % Rotamer: Outliers : 0.69 % Allowed : 18.06 % Favored : 81.25 % 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: 4.88 (0.38), residues: 506 helix: 4.03 (0.23), residues: 408 sheet: None (None), residues: 0 loop : -0.76 (0.71), residues: 98 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP U 95 HIS 0.003 0.000 HIS A 64 PHE 0.006 0.001 PHE A 97 TYR 0.012 0.001 TYR A 195 ARG 0.003 0.000 ARG U 292 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4360.05 seconds wall clock time: 75 minutes 2.53 seconds (4502.53 seconds total)