Starting phenix.real_space_refine on Sat May 10 07:27:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8w5m_37297/05_2025/8w5m_37297.cif Found real_map, /net/cci-nas-00/data/ceres_data/8w5m_37297/05_2025/8w5m_37297.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8w5m_37297/05_2025/8w5m_37297.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8w5m_37297/05_2025/8w5m_37297.map" model { file = "/net/cci-nas-00/data/ceres_data/8w5m_37297/05_2025/8w5m_37297.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8w5m_37297/05_2025/8w5m_37297.cif" } resolution = 3.1 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= 0.005 sd= 0.078 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 3519 2.51 5 N 995 2.21 5 O 1116 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 9 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 5645 Number of models: 1 Model: "" Number of chains: 6 Chain: "L" Number of atoms: 777 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 777 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 4, 'TRANS': 101} Chain: "H" Number of atoms: 924 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 924 Classifications: {'peptide': 119} Link IDs: {'PTRANS': 2, 'TRANS': 116} Chain: "A" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Chain: "b" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "B" Number of atoms: 992 Number of conformers: 1 Conformer: "" Number of residues, atoms: 132, 992 Classifications: {'peptide': 132} Link IDs: {'PTRANS': 8, 'TRANS': 123} Chain: "C" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 131, 980 Classifications: {'peptide': 131} Link IDs: {'PTRANS': 8, 'TRANS': 122} Time building chain proxies: 3.57, per 1000 atoms: 0.63 Number of scatterers: 5645 At special positions: 0 Unit cell: (101.64, 109.56, 89.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 1116 8.00 N 995 7.00 C 3519 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS L 25 " - pdb=" SG CYS L 93 " distance=2.03 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: 1.26 Conformation dependent library (CDL) restraints added in 692.1 milliseconds 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1388 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 12.8% alpha, 34.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 101 through 116 removed outlier: 3.583A pdb=" N ARG A 105 " --> pdb=" O THR A 101 " (cutoff:3.500A) Processing helix chain 'A' and resid 118 through 125 Processing helix chain 'b' and resid 101 through 116 removed outlier: 3.583A pdb=" N ARG b 105 " --> pdb=" O THR b 101 " (cutoff:3.500A) Processing helix chain 'b' and resid 118 through 125 Processing helix chain 'B' and resid 101 through 116 removed outlier: 3.584A pdb=" N ARG B 105 " --> pdb=" O THR B 101 " (cutoff:3.500A) Processing helix chain 'B' and resid 118 through 125 Processing helix chain 'C' and resid 101 through 116 removed outlier: 3.584A pdb=" N ARG C 105 " --> pdb=" O THR C 101 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 125 Processing sheet with id=AA1, first strand: chain 'L' and resid 8 through 9 Processing sheet with id=AA2, first strand: chain 'L' and resid 21 through 22 Processing sheet with id=AA3, first strand: chain 'L' and resid 48 through 53 removed outlier: 6.584A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 94 through 96 Processing sheet with id=AA5, first strand: chain 'H' and resid 7 through 10 removed outlier: 3.842A pdb=" N LEU H 7 " --> pdb=" O ALA H 26 " (cutoff:3.500A) removed outlier: 3.680A pdb=" N GLU H 9 " --> pdb=" O SER H 24 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N SER H 24 " --> pdb=" O GLU H 9 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N SER H 74 " --> pdb=" O PHE H 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 50 through 54 removed outlier: 6.874A pdb=" N TRP H 39 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N TYR H 53 " --> pdb=" O MET H 37 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N MET H 37 " --> pdb=" O TYR H 53 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N ARG H 42 " --> pdb=" O MET H 96 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N MET H 96 " --> pdb=" O ARG H 42 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N ALA H 95 " --> pdb=" O LEU H 119 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR H 117 " --> pdb=" O TYR H 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 6 through 11 removed outlier: 5.243A pdb=" N THR A 7 " --> pdb=" O LEU A 21 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU A 21 " --> pdb=" O THR A 7 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY A 9 " --> pdb=" O LEU A 19 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU A 19 " --> pdb=" O GLY A 9 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER A 34 " --> pdb=" O ARG A 24 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL A 26 " --> pdb=" O VAL A 32 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL A 32 " --> pdb=" O VAL A 26 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG A 86 " --> pdb=" O THR A 72 " (cutoff:3.500A) removed outlier: 6.886A pdb=" N CYS A 74 " --> pdb=" O VAL A 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL A 84 " --> pdb=" O CYS A 74 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N SER b 95 " --> pdb=" O TYR A 89 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL b 84 " --> pdb=" O CYS b 74 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS b 74 " --> pdb=" O VAL b 84 " (cutoff:3.500A) removed outlier: 3.967A pdb=" N ARG b 86 " --> pdb=" O THR b 72 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL b 32 " --> pdb=" O VAL b 26 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL b 26 " --> pdb=" O VAL b 32 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER b 34 " --> pdb=" O ARG b 24 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU b 19 " --> pdb=" O GLY b 9 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY b 9 " --> pdb=" O LEU b 19 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU b 21 " --> pdb=" O THR b 7 " (cutoff:3.500A) removed outlier: 5.246A pdb=" N THR b 7 " --> pdb=" O LEU b 21 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 6 through 11 removed outlier: 5.243A pdb=" N THR B 7 " --> pdb=" O LEU B 21 " (cutoff:3.500A) removed outlier: 7.092A pdb=" N LEU B 21 " --> pdb=" O THR B 7 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N GLY B 9 " --> pdb=" O LEU B 19 " (cutoff:3.500A) removed outlier: 6.746A pdb=" N LEU B 19 " --> pdb=" O GLY B 9 " (cutoff:3.500A) removed outlier: 5.168A pdb=" N SER B 34 " --> pdb=" O ARG B 24 " (cutoff:3.500A) removed outlier: 4.907A pdb=" N VAL B 26 " --> pdb=" O VAL B 32 " (cutoff:3.500A) removed outlier: 6.110A pdb=" N VAL B 32 " --> pdb=" O VAL B 26 " (cutoff:3.500A) removed outlier: 3.968A pdb=" N ARG B 86 " --> pdb=" O THR B 72 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS B 74 " --> pdb=" O VAL B 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL B 84 " --> pdb=" O CYS B 74 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 6 through 11 removed outlier: 5.244A pdb=" N THR C 7 " --> pdb=" O LEU C 21 " (cutoff:3.500A) removed outlier: 7.093A pdb=" N LEU C 21 " --> pdb=" O THR C 7 " (cutoff:3.500A) removed outlier: 5.367A pdb=" N GLY C 9 " --> pdb=" O LEU C 19 " (cutoff:3.500A) removed outlier: 6.747A pdb=" N LEU C 19 " --> pdb=" O GLY C 9 " (cutoff:3.500A) removed outlier: 5.169A pdb=" N SER C 34 " --> pdb=" O ARG C 24 " (cutoff:3.500A) removed outlier: 4.906A pdb=" N VAL C 26 " --> pdb=" O VAL C 32 " (cutoff:3.500A) removed outlier: 6.111A pdb=" N VAL C 32 " --> pdb=" O VAL C 26 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N ARG C 86 " --> pdb=" O THR C 72 " (cutoff:3.500A) removed outlier: 6.885A pdb=" N CYS C 74 " --> pdb=" O VAL C 84 " (cutoff:3.500A) removed outlier: 5.881A pdb=" N VAL C 84 " --> pdb=" O CYS C 74 " (cutoff:3.500A) 211 hydrogen bonds defined for protein. 582 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: 1.26 Time building geometry restraints manager: 1.49 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.16 - 1.29: 958 1.29 - 1.42: 1378 1.42 - 1.55: 3372 1.55 - 1.68: 14 1.68 - 1.81: 18 Bond restraints: 5740 Sorted by residual: bond pdb=" C VAL A 6 " pdb=" O VAL A 6 " ideal model delta sigma weight residual 1.236 1.156 0.081 1.20e-02 6.94e+03 4.53e+01 bond pdb=" C LEU A 3 " pdb=" O LEU A 3 " ideal model delta sigma weight residual 1.235 1.169 0.066 1.20e-02 6.94e+03 2.99e+01 bond pdb=" C THR A 5 " pdb=" O THR A 5 " ideal model delta sigma weight residual 1.234 1.171 0.063 1.20e-02 6.94e+03 2.76e+01 bond pdb=" CB THR A 5 " pdb=" CG2 THR A 5 " ideal model delta sigma weight residual 1.521 1.377 0.144 3.30e-02 9.18e+02 1.90e+01 bond pdb=" CA THR A 5 " pdb=" CB THR A 5 " ideal model delta sigma weight residual 1.529 1.461 0.068 1.64e-02 3.72e+03 1.70e+01 ... (remaining 5735 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.20: 7509 2.20 - 4.39: 249 4.39 - 6.59: 35 6.59 - 8.79: 13 8.79 - 10.98: 7 Bond angle restraints: 7813 Sorted by residual: angle pdb=" C SER C 53 " pdb=" N GLN C 54 " pdb=" CA GLN C 54 " ideal model delta sigma weight residual 120.86 130.18 -9.32 1.60e+00 3.91e-01 3.39e+01 angle pdb=" C SER b 53 " pdb=" N GLN b 54 " pdb=" CA GLN b 54 " ideal model delta sigma weight residual 120.86 130.16 -9.30 1.60e+00 3.91e-01 3.38e+01 angle pdb=" C SER B 53 " pdb=" N GLN B 54 " pdb=" CA GLN B 54 " ideal model delta sigma weight residual 120.86 130.15 -9.29 1.60e+00 3.91e-01 3.37e+01 angle pdb=" C SER A 53 " pdb=" N GLN A 54 " pdb=" CA GLN A 54 " ideal model delta sigma weight residual 120.86 130.13 -9.27 1.60e+00 3.91e-01 3.36e+01 angle pdb=" N VAL A 6 " pdb=" CA VAL A 6 " pdb=" CB VAL A 6 " ideal model delta sigma weight residual 111.83 105.69 6.14 1.23e+00 6.61e-01 2.49e+01 ... (remaining 7808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.03: 3316 14.03 - 28.06: 123 28.06 - 42.09: 29 42.09 - 56.12: 0 56.12 - 70.15: 4 Dihedral angle restraints: 3472 sinusoidal: 1315 harmonic: 2157 Sorted by residual: dihedral pdb=" CA GLY L 18 " pdb=" C GLY L 18 " pdb=" N GLU L 19 " pdb=" CA GLU L 19 " ideal model delta harmonic sigma weight residual 180.00 141.49 38.51 0 5.00e+00 4.00e-02 5.93e+01 dihedral pdb=" CA ASP H 65 " pdb=" C ASP H 65 " pdb=" N THR H 66 " pdb=" CA THR H 66 " ideal model delta harmonic sigma weight residual 180.00 151.56 28.44 0 5.00e+00 4.00e-02 3.24e+01 dihedral pdb=" CA CYS H 99 " pdb=" C CYS H 99 " pdb=" N ALA H 100 " pdb=" CA ALA H 100 " ideal model delta harmonic sigma weight residual -180.00 -151.88 -28.12 0 5.00e+00 4.00e-02 3.16e+01 ... (remaining 3469 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 599 0.050 - 0.101: 217 0.101 - 0.151: 74 0.151 - 0.201: 20 0.201 - 0.251: 11 Chirality restraints: 921 Sorted by residual: chirality pdb=" CA VAL A 6 " pdb=" N VAL A 6 " pdb=" C VAL A 6 " pdb=" CB VAL A 6 " both_signs ideal model delta sigma weight residual False 2.44 2.69 -0.25 2.00e-01 2.50e+01 1.58e+00 chirality pdb=" CG LEU b 128 " pdb=" CB LEU b 128 " pdb=" CD1 LEU b 128 " pdb=" CD2 LEU b 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CG LEU C 128 " pdb=" CB LEU C 128 " pdb=" CD1 LEU C 128 " pdb=" CD2 LEU C 128 " both_signs ideal model delta sigma weight residual False -2.59 -2.36 -0.23 2.00e-01 2.50e+01 1.28e+00 ... (remaining 918 not shown) Planarity restraints: 1021 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY L 18 " -0.013 2.00e-02 2.50e+03 2.66e-02 7.09e+00 pdb=" C GLY L 18 " 0.046 2.00e-02 2.50e+03 pdb=" O GLY L 18 " -0.017 2.00e-02 2.50e+03 pdb=" N GLU L 19 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL H 67 " -0.013 2.00e-02 2.50e+03 2.51e-02 6.30e+00 pdb=" C VAL H 67 " 0.043 2.00e-02 2.50e+03 pdb=" O VAL H 67 " -0.016 2.00e-02 2.50e+03 pdb=" N LYS H 68 " -0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL b 41 " 0.040 5.00e-02 4.00e+02 6.13e-02 6.01e+00 pdb=" N PRO b 42 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO b 42 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO b 42 " 0.033 5.00e-02 4.00e+02 ... (remaining 1018 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1364 2.80 - 3.32: 4481 3.32 - 3.85: 8661 3.85 - 4.37: 9553 4.37 - 4.90: 17345 Nonbonded interactions: 41404 Sorted by model distance: nonbonded pdb=" N ALA A 1 " pdb=" OD2 ASP b 123 " model vdw 2.272 3.120 nonbonded pdb=" OG1 THR H 72 " pdb=" O GLN H 85 " model vdw 2.329 3.040 nonbonded pdb=" O ASP H 105 " pdb=" OH TYR H 109 " model vdw 2.369 3.040 nonbonded pdb=" OE1 GLN B 87 " pdb=" OH TYR B 89 " model vdw 2.402 3.040 nonbonded pdb=" OE1 GLN A 87 " pdb=" OH TYR A 89 " model vdw 2.402 3.040 ... (remaining 41399 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' selection = (chain 'B' and resid 1 through 131) selection = chain 'C' selection = (chain 'b' and resid 1 through 131) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.380 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: 0.040 Set scattering table: 0.060 Process input model: 16.000 Find NCS groups from input model: 0.170 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.144 5741 Z= 0.309 Angle : 0.981 10.984 7815 Z= 0.546 Chirality : 0.063 0.251 921 Planarity : 0.008 0.061 1021 Dihedral : 8.719 70.155 2081 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 6.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer: Outliers : 0.16 % Allowed : 4.38 % Favored : 95.45 % Cbeta Deviations : 0.29 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.14 % 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: -3.59 (0.26), residues: 739 helix: -2.05 (0.44), residues: 92 sheet: -1.48 (0.29), residues: 301 loop : -3.34 (0.22), residues: 346 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP H 113 HIS 0.008 0.003 HIS H 107 PHE 0.024 0.003 PHE H 71 TYR 0.021 0.003 TYR b 62 ARG 0.025 0.001 ARG H 102 Details of bonding type rmsd hydrogen bonds : bond 0.14308 ( 211) hydrogen bonds : angle 6.66526 ( 582) SS BOND : bond 0.00060 ( 1) SS BOND : angle 0.41650 ( 2) covalent geometry : bond 0.00578 ( 5740) covalent geometry : angle 0.98160 ( 7813) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 162 time to evaluate : 0.631 Fit side-chains REVERT: L 72 ILE cc_start: 0.9129 (mt) cc_final: 0.8779 (pt) REVERT: L 102 VAL cc_start: 0.8596 (t) cc_final: 0.8395 (m) REVERT: H 21 LEU cc_start: 0.7344 (OUTLIER) cc_final: 0.7021 (tm) REVERT: H 74 SER cc_start: 0.8886 (t) cc_final: 0.8254 (p) REVERT: A 53 SER cc_start: 0.8085 (m) cc_final: 0.7660 (t) REVERT: b 2 LYS cc_start: 0.7997 (tttt) cc_final: 0.7516 (mmtt) REVERT: b 24 ARG cc_start: 0.8211 (mtp180) cc_final: 0.6545 (tpt170) REVERT: b 53 SER cc_start: 0.8613 (m) cc_final: 0.8399 (t) REVERT: b 60 LYS cc_start: 0.8426 (pttm) cc_final: 0.8221 (ptpp) REVERT: b 102 ASP cc_start: 0.8366 (p0) cc_final: 0.8134 (p0) REVERT: C 34 SER cc_start: 0.8797 (m) cc_final: 0.8546 (t) outliers start: 1 outliers final: 0 residues processed: 162 average time/residue: 0.1915 time to fit residues: 38.7694 Evaluate side-chains 111 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 110 time to evaluate : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 21 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 10.0000 chunk 37 optimal weight: 9.9990 chunk 29 optimal weight: 0.9990 chunk 57 optimal weight: 0.9990 chunk 22 optimal weight: 3.9990 chunk 34 optimal weight: 4.9990 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 6.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 36 ASN L 57 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 22 ASN b 61 ASN b 77 ASN B 61 ASN C 61 ASN C 70 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138711 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.106070 restraints weight = 7361.483| |-----------------------------------------------------------------------------| r_work (start): 0.3302 rms_B_bonded: 2.74 r_work: 0.3153 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5741 Z= 0.145 Angle : 0.607 7.861 7815 Z= 0.320 Chirality : 0.047 0.143 921 Planarity : 0.005 0.048 1021 Dihedral : 5.097 37.929 808 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 7.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.87 % Favored : 95.13 % Rotamer: Outliers : 2.60 % Allowed : 9.42 % Favored : 87.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.28), residues: 739 helix: -0.46 (0.53), residues: 94 sheet: -0.95 (0.28), residues: 323 loop : -3.06 (0.25), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 113 HIS 0.007 0.002 HIS H 108 PHE 0.017 0.002 PHE H 71 TYR 0.015 0.002 TYR H 63 ARG 0.006 0.001 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.04229 ( 211) hydrogen bonds : angle 5.23580 ( 582) SS BOND : bond 0.00044 ( 1) SS BOND : angle 0.63649 ( 2) covalent geometry : bond 0.00332 ( 5740) covalent geometry : angle 0.60719 ( 7813) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 125 time to evaluate : 0.572 Fit side-chains REVERT: L 23 LEU cc_start: 0.8486 (mp) cc_final: 0.8214 (mp) REVERT: L 72 ILE cc_start: 0.9187 (mt) cc_final: 0.8835 (pt) REVERT: H 25 CYS cc_start: 0.7975 (p) cc_final: 0.7619 (t) REVERT: H 85 GLN cc_start: 0.7557 (tp40) cc_final: 0.7015 (tp-100) REVERT: b 2 LYS cc_start: 0.8221 (tttt) cc_final: 0.7614 (mmtt) REVERT: b 24 ARG cc_start: 0.8723 (mtp180) cc_final: 0.6346 (tpt170) REVERT: b 60 LYS cc_start: 0.8874 (pttm) cc_final: 0.8446 (ptpp) REVERT: b 123 ASP cc_start: 0.8986 (t70) cc_final: 0.8557 (t0) REVERT: b 127 GLN cc_start: 0.8900 (mp10) cc_final: 0.8680 (mm110) REVERT: B 47 ARG cc_start: 0.8259 (ptp-170) cc_final: 0.7921 (ptp-110) REVERT: C 16 LYS cc_start: 0.9203 (mttt) cc_final: 0.8856 (mttt) REVERT: C 45 GLU cc_start: 0.8243 (mm-30) cc_final: 0.8040 (mm-30) outliers start: 16 outliers final: 9 residues processed: 136 average time/residue: 0.2179 time to fit residues: 36.4458 Evaluate side-chains 113 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 104 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 67 VAL Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain C residue 7 THR Chi-restraints excluded: chain C residue 51 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 47 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 65 optimal weight: 7.9990 chunk 15 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 64 optimal weight: 1.9990 chunk 59 optimal weight: 0.6980 chunk 11 optimal weight: 30.0000 chunk 19 optimal weight: 7.9990 chunk 68 optimal weight: 0.8980 chunk 52 optimal weight: 8.9990 overall best weight: 0.9160 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 6 GLN ** A 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** b 22 ASN B 22 ASN C 22 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3704 r_free = 0.3704 target = 0.138751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.106551 restraints weight = 7414.697| |-----------------------------------------------------------------------------| r_work (start): 0.3309 rms_B_bonded: 2.71 r_work: 0.3158 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work: 0.3018 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.3018 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.3244 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 5741 Z= 0.105 Angle : 0.528 6.915 7815 Z= 0.279 Chirality : 0.045 0.141 921 Planarity : 0.004 0.039 1021 Dihedral : 4.522 30.282 808 Min Nonbonded Distance : 2.618 Molprobity Statistics. All-atom Clashscore : 6.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Rotamer: Outliers : 3.25 % Allowed : 11.85 % Favored : 84.90 % 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: -1.79 (0.29), residues: 739 helix: 0.35 (0.56), residues: 94 sheet: -0.20 (0.30), residues: 289 loop : -2.54 (0.27), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 113 HIS 0.004 0.001 HIS H 108 PHE 0.013 0.001 PHE H 71 TYR 0.007 0.001 TYR B 62 ARG 0.006 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.03691 ( 211) hydrogen bonds : angle 4.75299 ( 582) SS BOND : bond 0.00066 ( 1) SS BOND : angle 0.70837 ( 2) covalent geometry : bond 0.00226 ( 5740) covalent geometry : angle 0.52801 ( 7813) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 115 time to evaluate : 0.633 Fit side-chains revert: symmetry clash REVERT: L 23 LEU cc_start: 0.8407 (mp) cc_final: 0.8099 (mp) REVERT: L 72 ILE cc_start: 0.9109 (mt) cc_final: 0.8814 (pt) REVERT: H 21 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7010 (tm) REVERT: H 25 CYS cc_start: 0.8174 (p) cc_final: 0.7881 (t) REVERT: H 71 PHE cc_start: 0.8316 (m-10) cc_final: 0.8093 (m-10) REVERT: H 102 ARG cc_start: 0.8725 (ttt90) cc_final: 0.7990 (ttt90) REVERT: A 45 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8202 (mt-10) REVERT: b 2 LYS cc_start: 0.8348 (tttt) cc_final: 0.7656 (mmtt) REVERT: b 16 LYS cc_start: 0.9104 (OUTLIER) cc_final: 0.8626 (mtmp) REVERT: b 24 ARG cc_start: 0.8881 (mtp180) cc_final: 0.6331 (tpt170) REVERT: b 60 LYS cc_start: 0.8903 (pttm) cc_final: 0.8469 (ptpp) REVERT: b 123 ASP cc_start: 0.9087 (t70) cc_final: 0.8764 (t0) REVERT: B 20 VAL cc_start: 0.9145 (OUTLIER) cc_final: 0.8853 (t) REVERT: B 47 ARG cc_start: 0.8350 (ptp-170) cc_final: 0.8093 (ptp-110) REVERT: C 16 LYS cc_start: 0.9265 (mttt) cc_final: 0.9044 (mttt) REVERT: C 45 GLU cc_start: 0.8369 (mm-30) cc_final: 0.8119 (mm-30) REVERT: C 93 THR cc_start: 0.9273 (OUTLIER) cc_final: 0.9058 (m) REVERT: C 127 GLN cc_start: 0.9004 (mp10) cc_final: 0.8551 (mp10) outliers start: 20 outliers final: 10 residues processed: 131 average time/residue: 0.2051 time to fit residues: 33.6382 Evaluate side-chains 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 102 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 115 GLN Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 16 LYS Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 93 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 3.9990 chunk 7 optimal weight: 9.9990 chunk 69 optimal weight: 7.9990 chunk 9 optimal weight: 8.9990 chunk 40 optimal weight: 7.9990 chunk 36 optimal weight: 9.9990 chunk 67 optimal weight: 9.9990 chunk 59 optimal weight: 5.9990 chunk 25 optimal weight: 8.9990 chunk 66 optimal weight: 3.9990 chunk 5 optimal weight: 10.0000 overall best weight: 5.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 69 GLN ** b 70 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.126951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095009 restraints weight = 7621.338| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.67 r_work: 0.2986 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2846 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2846 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8437 moved from start: 0.4128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.060 5741 Z= 0.377 Angle : 0.735 5.679 7815 Z= 0.394 Chirality : 0.056 0.166 921 Planarity : 0.005 0.045 1021 Dihedral : 5.450 38.032 808 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer: Outliers : 4.22 % Allowed : 12.66 % Favored : 83.12 % 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: -2.34 (0.28), residues: 739 helix: -0.64 (0.53), residues: 96 sheet: -0.70 (0.28), residues: 329 loop : -2.78 (0.27), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 113 HIS 0.007 0.003 HIS L 100 PHE 0.012 0.002 PHE H 98 TYR 0.029 0.003 TYR B 62 ARG 0.008 0.001 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.05094 ( 211) hydrogen bonds : angle 5.31475 ( 582) SS BOND : bond 0.00467 ( 1) SS BOND : angle 2.09028 ( 2) covalent geometry : bond 0.00901 ( 5740) covalent geometry : angle 0.73439 ( 7813) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 139 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 113 time to evaluate : 0.575 Fit side-chains REVERT: L 47 HIS cc_start: 0.7772 (p-80) cc_final: 0.7485 (p-80) REVERT: A 45 GLU cc_start: 0.8660 (mt-10) cc_final: 0.8368 (mt-10) REVERT: A 123 ASP cc_start: 0.8887 (t70) cc_final: 0.8456 (t0) REVERT: b 2 LYS cc_start: 0.8542 (tttt) cc_final: 0.7806 (mmtt) REVERT: b 24 ARG cc_start: 0.9178 (mtp180) cc_final: 0.7223 (tpt170) REVERT: b 60 LYS cc_start: 0.8987 (pttm) cc_final: 0.8651 (ptpp) REVERT: b 123 ASP cc_start: 0.9211 (t70) cc_final: 0.8792 (t0) REVERT: B 61 ASN cc_start: 0.8626 (m-40) cc_final: 0.8392 (m-40) REVERT: C 2 LYS cc_start: 0.8574 (tttt) cc_final: 0.6484 (mmtt) REVERT: C 45 GLU cc_start: 0.8493 (mm-30) cc_final: 0.8225 (mm-30) REVERT: C 87 GLN cc_start: 0.9114 (mt0) cc_final: 0.8810 (mt0) REVERT: C 122 ILE cc_start: 0.8716 (pt) cc_final: 0.8131 (mm) outliers start: 26 outliers final: 19 residues processed: 132 average time/residue: 0.1975 time to fit residues: 32.6304 Evaluate side-chains 126 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 29 THR Chi-restraints excluded: chain L residue 74 ASP Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain b residue 122 ILE Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 27 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 0.3980 chunk 26 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 6.9990 chunk 71 optimal weight: 0.9990 chunk 40 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 12 optimal weight: 10.0000 chunk 3 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.126674 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.096046 restraints weight = 7426.378| |-----------------------------------------------------------------------------| r_work (start): 0.3117 rms_B_bonded: 2.54 r_work: 0.2998 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8254 moved from start: 0.4216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5741 Z= 0.116 Angle : 0.540 6.176 7815 Z= 0.287 Chirality : 0.046 0.150 921 Planarity : 0.004 0.041 1021 Dihedral : 4.631 28.477 808 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.90 % Allowed : 13.31 % Favored : 82.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.95 (0.29), residues: 739 helix: 0.10 (0.55), residues: 96 sheet: -0.40 (0.29), residues: 324 loop : -2.74 (0.26), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 113 HIS 0.005 0.001 HIS H 108 PHE 0.012 0.001 PHE H 71 TYR 0.010 0.001 TYR L 37 ARG 0.007 0.000 ARG B 57 Details of bonding type rmsd hydrogen bonds : bond 0.03676 ( 211) hydrogen bonds : angle 4.76898 ( 582) SS BOND : bond 0.00086 ( 1) SS BOND : angle 0.78070 ( 2) covalent geometry : bond 0.00263 ( 5740) covalent geometry : angle 0.54001 ( 7813) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 106 time to evaluate : 0.646 Fit side-chains revert: symmetry clash REVERT: L 72 ILE cc_start: 0.9100 (mt) cc_final: 0.8740 (pt) REVERT: H 21 LEU cc_start: 0.7390 (OUTLIER) cc_final: 0.6742 (tm) REVERT: H 105 ASP cc_start: 0.7557 (OUTLIER) cc_final: 0.7212 (t0) REVERT: A 45 GLU cc_start: 0.8611 (mt-10) cc_final: 0.8317 (mt-10) REVERT: b 2 LYS cc_start: 0.8458 (tttt) cc_final: 0.7750 (mmtt) REVERT: b 24 ARG cc_start: 0.8989 (mtp180) cc_final: 0.6385 (tpt170) REVERT: b 60 LYS cc_start: 0.8917 (pttm) cc_final: 0.8558 (ptpp) REVERT: b 123 ASP cc_start: 0.9188 (t70) cc_final: 0.8747 (t0) REVERT: B 47 ARG cc_start: 0.8353 (ptp90) cc_final: 0.8078 (ptp-110) REVERT: B 61 ASN cc_start: 0.8601 (m-40) cc_final: 0.8268 (m-40) REVERT: C 2 LYS cc_start: 0.8463 (tttt) cc_final: 0.6479 (mmtt) REVERT: C 45 GLU cc_start: 0.8441 (mm-30) cc_final: 0.7950 (mm-30) REVERT: C 87 GLN cc_start: 0.9208 (mt0) cc_final: 0.8904 (mt0) REVERT: C 93 THR cc_start: 0.9389 (OUTLIER) cc_final: 0.9184 (t) REVERT: C 121 LEU cc_start: 0.8707 (mm) cc_final: 0.8390 (mt) REVERT: C 122 ILE cc_start: 0.8540 (pt) cc_final: 0.8038 (mm) outliers start: 24 outliers final: 12 residues processed: 126 average time/residue: 0.2009 time to fit residues: 31.7212 Evaluate side-chains 115 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 100 time to evaluate : 0.621 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Chi-restraints excluded: chain C residue 93 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 24 optimal weight: 10.0000 chunk 15 optimal weight: 1.9990 chunk 26 optimal weight: 0.0870 chunk 27 optimal weight: 0.9980 chunk 46 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 7 optimal weight: 9.9990 chunk 67 optimal weight: 0.4980 chunk 23 optimal weight: 2.9990 chunk 44 optimal weight: 7.9990 chunk 38 optimal weight: 4.9990 overall best weight: 1.3162 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN B 10 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.126847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.096306 restraints weight = 7404.936| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 2.55 r_work: 0.3003 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8253 moved from start: 0.4323 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5741 Z= 0.116 Angle : 0.536 7.143 7815 Z= 0.283 Chirality : 0.046 0.149 921 Planarity : 0.004 0.043 1021 Dihedral : 4.417 29.285 808 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 5.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 4.22 % Allowed : 14.29 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.29), residues: 739 helix: 0.36 (0.56), residues: 96 sheet: -0.12 (0.30), residues: 301 loop : -2.47 (0.27), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 113 HIS 0.004 0.001 HIS H 108 PHE 0.018 0.001 PHE H 71 TYR 0.010 0.001 TYR B 62 ARG 0.005 0.000 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.03609 ( 211) hydrogen bonds : angle 4.60692 ( 582) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.79281 ( 2) covalent geometry : bond 0.00262 ( 5740) covalent geometry : angle 0.53577 ( 7813) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 101 time to evaluate : 1.154 Fit side-chains revert: symmetry clash REVERT: L 72 ILE cc_start: 0.9188 (mt) cc_final: 0.8853 (pt) REVERT: H 21 LEU cc_start: 0.7408 (OUTLIER) cc_final: 0.6699 (tm) REVERT: H 96 MET cc_start: 0.6138 (mtm) cc_final: 0.5704 (ttt) REVERT: H 105 ASP cc_start: 0.7592 (OUTLIER) cc_final: 0.7232 (t0) REVERT: A 45 GLU cc_start: 0.8618 (mt-10) cc_final: 0.8348 (mt-10) REVERT: b 2 LYS cc_start: 0.8463 (tttt) cc_final: 0.7756 (mmtt) REVERT: b 24 ARG cc_start: 0.9004 (mtp180) cc_final: 0.6263 (tpt170) REVERT: b 60 LYS cc_start: 0.8922 (pttm) cc_final: 0.8559 (ptpp) REVERT: b 123 ASP cc_start: 0.9199 (t70) cc_final: 0.8773 (t0) REVERT: B 47 ARG cc_start: 0.8344 (ptp90) cc_final: 0.8066 (ptp-110) REVERT: B 61 ASN cc_start: 0.8604 (m-40) cc_final: 0.8219 (m-40) REVERT: C 2 LYS cc_start: 0.8481 (tttt) cc_final: 0.6469 (mmtt) REVERT: C 87 GLN cc_start: 0.9170 (mt0) cc_final: 0.8927 (mt0) REVERT: C 121 LEU cc_start: 0.8695 (mm) cc_final: 0.8386 (mt) REVERT: C 122 ILE cc_start: 0.8442 (pt) cc_final: 0.7964 (mm) outliers start: 26 outliers final: 15 residues processed: 122 average time/residue: 0.1947 time to fit residues: 30.2604 Evaluate side-chains 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.703 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 67 optimal weight: 0.0070 chunk 65 optimal weight: 2.9990 chunk 12 optimal weight: 10.0000 chunk 62 optimal weight: 6.9990 chunk 20 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 61 optimal weight: 1.9990 chunk 25 optimal weight: 8.9990 chunk 26 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 overall best weight: 1.3002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3524 r_free = 0.3524 target = 0.127818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.097339 restraints weight = 7430.421| |-----------------------------------------------------------------------------| r_work (start): 0.3129 rms_B_bonded: 2.54 r_work: 0.3013 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2883 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2883 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.4423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5741 Z= 0.114 Angle : 0.532 7.243 7815 Z= 0.280 Chirality : 0.046 0.146 921 Planarity : 0.004 0.039 1021 Dihedral : 4.296 27.773 808 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.74 % Favored : 95.26 % Rotamer: Outliers : 2.92 % Allowed : 15.58 % Favored : 81.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.29), residues: 739 helix: 0.48 (0.56), residues: 96 sheet: 0.03 (0.30), residues: 295 loop : -2.42 (0.26), residues: 348 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 113 HIS 0.004 0.001 HIS H 108 PHE 0.006 0.001 PHE L 49 TYR 0.009 0.001 TYR B 62 ARG 0.006 0.000 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.03561 ( 211) hydrogen bonds : angle 4.53974 ( 582) SS BOND : bond 0.00130 ( 1) SS BOND : angle 0.81965 ( 2) covalent geometry : bond 0.00259 ( 5740) covalent geometry : angle 0.53160 ( 7813) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 121 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 103 time to evaluate : 0.633 Fit side-chains REVERT: L 72 ILE cc_start: 0.9118 (mt) cc_final: 0.8853 (pt) REVERT: H 21 LEU cc_start: 0.7737 (OUTLIER) cc_final: 0.7039 (tm) REVERT: H 105 ASP cc_start: 0.7553 (OUTLIER) cc_final: 0.7186 (t0) REVERT: b 2 LYS cc_start: 0.8485 (tttt) cc_final: 0.7703 (mmtt) REVERT: b 4 GLU cc_start: 0.8172 (pt0) cc_final: 0.7717 (mt-10) REVERT: b 24 ARG cc_start: 0.9010 (mtp180) cc_final: 0.6256 (tpt170) REVERT: b 60 LYS cc_start: 0.8917 (pttm) cc_final: 0.8561 (ptpp) REVERT: b 123 ASP cc_start: 0.9186 (t70) cc_final: 0.8751 (t0) REVERT: B 47 ARG cc_start: 0.8315 (ptp90) cc_final: 0.8056 (ptp-110) REVERT: B 61 ASN cc_start: 0.8599 (m-40) cc_final: 0.8220 (m-40) REVERT: C 2 LYS cc_start: 0.8481 (tttt) cc_final: 0.6464 (mmtt) REVERT: C 87 GLN cc_start: 0.9111 (mt0) cc_final: 0.8815 (mt0) REVERT: C 121 LEU cc_start: 0.8685 (mm) cc_final: 0.8367 (mt) REVERT: C 122 ILE cc_start: 0.8433 (pt) cc_final: 0.7948 (mm) outliers start: 18 outliers final: 13 residues processed: 117 average time/residue: 0.2022 time to fit residues: 29.9695 Evaluate side-chains 116 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 101 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 0.3980 chunk 67 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 33 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 59 optimal weight: 0.8980 chunk 57 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 36 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 2 optimal weight: 30.0000 overall best weight: 1.6582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3510 r_free = 0.3510 target = 0.126792 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.096408 restraints weight = 7315.328| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.52 r_work: 0.3001 rms_B_bonded: 2.73 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 4.45 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5741 Z= 0.128 Angle : 0.536 6.609 7815 Z= 0.283 Chirality : 0.047 0.143 921 Planarity : 0.004 0.043 1021 Dihedral : 4.322 28.459 808 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 5.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.57 % Allowed : 15.58 % Favored : 80.84 % 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: -1.54 (0.29), residues: 739 helix: 0.44 (0.55), residues: 96 sheet: -0.05 (0.30), residues: 306 loop : -2.47 (0.26), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 113 HIS 0.003 0.001 HIS H 108 PHE 0.007 0.001 PHE H 71 TYR 0.012 0.001 TYR B 62 ARG 0.004 0.000 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.03700 ( 211) hydrogen bonds : angle 4.56807 ( 582) SS BOND : bond 0.00181 ( 1) SS BOND : angle 0.96243 ( 2) covalent geometry : bond 0.00295 ( 5740) covalent geometry : angle 0.53600 ( 7813) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 101 time to evaluate : 0.519 Fit side-chains REVERT: L 72 ILE cc_start: 0.9101 (mt) cc_final: 0.8836 (pt) REVERT: H 21 LEU cc_start: 0.7454 (OUTLIER) cc_final: 0.6763 (tm) REVERT: H 105 ASP cc_start: 0.7576 (OUTLIER) cc_final: 0.7204 (t0) REVERT: b 2 LYS cc_start: 0.8489 (tttt) cc_final: 0.7701 (mmtt) REVERT: b 4 GLU cc_start: 0.8188 (pt0) cc_final: 0.7729 (mt-10) REVERT: b 24 ARG cc_start: 0.8969 (mtp180) cc_final: 0.6279 (tpt170) REVERT: b 60 LYS cc_start: 0.8923 (pttm) cc_final: 0.8595 (ptpp) REVERT: b 123 ASP cc_start: 0.9192 (t70) cc_final: 0.8760 (t0) REVERT: B 47 ARG cc_start: 0.8388 (ptp90) cc_final: 0.8127 (ptp-110) REVERT: B 61 ASN cc_start: 0.8629 (m-40) cc_final: 0.8225 (m-40) REVERT: C 2 LYS cc_start: 0.8528 (tttt) cc_final: 0.6478 (mmtt) REVERT: C 16 LYS cc_start: 0.8950 (mttp) cc_final: 0.8706 (mttt) REVERT: C 87 GLN cc_start: 0.9116 (mt0) cc_final: 0.8795 (mt0) REVERT: C 121 LEU cc_start: 0.8691 (mm) cc_final: 0.8391 (mt) REVERT: C 122 ILE cc_start: 0.8490 (pt) cc_final: 0.7942 (mm) outliers start: 22 outliers final: 16 residues processed: 117 average time/residue: 0.1970 time to fit residues: 29.6973 Evaluate side-chains 119 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 101 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 64 optimal weight: 7.9990 chunk 54 optimal weight: 9.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 37 optimal weight: 9.9990 chunk 34 optimal weight: 6.9990 chunk 30 optimal weight: 0.9980 chunk 55 optimal weight: 0.0470 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 overall best weight: 1.4084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.127477 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3138 r_free = 0.3138 target = 0.097143 restraints weight = 7378.721| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.53 r_work: 0.3012 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.4580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5741 Z= 0.117 Angle : 0.527 7.084 7815 Z= 0.279 Chirality : 0.046 0.142 921 Planarity : 0.004 0.041 1021 Dihedral : 4.237 26.395 808 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 3.08 % Allowed : 16.40 % Favored : 80.52 % 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: -1.38 (0.29), residues: 739 helix: 0.53 (0.56), residues: 96 sheet: 0.09 (0.30), residues: 296 loop : -2.32 (0.27), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 113 HIS 0.004 0.001 HIS H 108 PHE 0.006 0.001 PHE H 71 TYR 0.010 0.001 TYR B 62 ARG 0.004 0.000 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.03585 ( 211) hydrogen bonds : angle 4.51794 ( 582) SS BOND : bond 0.00101 ( 1) SS BOND : angle 0.79083 ( 2) covalent geometry : bond 0.00267 ( 5740) covalent geometry : angle 0.52711 ( 7813) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 103 time to evaluate : 0.618 Fit side-chains REVERT: L 72 ILE cc_start: 0.9087 (mt) cc_final: 0.8846 (pt) REVERT: H 21 LEU cc_start: 0.7400 (OUTLIER) cc_final: 0.6614 (tm) REVERT: H 92 GLU cc_start: 0.7265 (pt0) cc_final: 0.6863 (pm20) REVERT: H 105 ASP cc_start: 0.7530 (OUTLIER) cc_final: 0.7157 (t0) REVERT: b 2 LYS cc_start: 0.8499 (tttt) cc_final: 0.7752 (mmtt) REVERT: b 4 GLU cc_start: 0.8189 (pt0) cc_final: 0.7749 (mt-10) REVERT: b 24 ARG cc_start: 0.8947 (mtp180) cc_final: 0.6273 (tpt170) REVERT: b 60 LYS cc_start: 0.8923 (pttm) cc_final: 0.8567 (ptpp) REVERT: b 123 ASP cc_start: 0.9192 (t70) cc_final: 0.8751 (t0) REVERT: B 47 ARG cc_start: 0.8301 (ptp90) cc_final: 0.8058 (ptp-110) REVERT: B 61 ASN cc_start: 0.8596 (m-40) cc_final: 0.8221 (m-40) REVERT: C 2 LYS cc_start: 0.8589 (tttt) cc_final: 0.6585 (mmtt) REVERT: C 87 GLN cc_start: 0.9109 (mt0) cc_final: 0.8845 (mt0) REVERT: C 121 LEU cc_start: 0.8649 (mm) cc_final: 0.8345 (mt) REVERT: C 122 ILE cc_start: 0.8469 (pt) cc_final: 0.7931 (mm) outliers start: 19 outliers final: 16 residues processed: 117 average time/residue: 0.1874 time to fit residues: 27.8810 Evaluate side-chains 120 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 102 time to evaluate : 0.648 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 53 TYR Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Chi-restraints excluded: chain C residue 85 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 5.9990 chunk 41 optimal weight: 4.9990 chunk 58 optimal weight: 7.9990 chunk 46 optimal weight: 2.9990 chunk 66 optimal weight: 7.9990 chunk 67 optimal weight: 5.9990 chunk 36 optimal weight: 7.9990 chunk 38 optimal weight: 2.9990 chunk 14 optimal weight: 0.0000 chunk 53 optimal weight: 6.9990 chunk 18 optimal weight: 10.0000 overall best weight: 3.3992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 107 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 115 GLN A 129 ASN C 98 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.123121 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.092960 restraints weight = 7682.893| |-----------------------------------------------------------------------------| r_work (start): 0.3065 rms_B_bonded: 2.51 r_work: 0.2947 rms_B_bonded: 2.72 restraints_weight: 0.5000 r_work: 0.2817 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2817 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5741 Z= 0.221 Angle : 0.605 7.472 7815 Z= 0.322 Chirality : 0.050 0.151 921 Planarity : 0.004 0.042 1021 Dihedral : 4.683 30.286 808 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.55 % Favored : 94.45 % Rotamer: Outliers : 3.08 % Allowed : 17.05 % Favored : 79.87 % 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: -1.68 (0.29), residues: 739 helix: 0.05 (0.54), residues: 96 sheet: -0.23 (0.29), residues: 320 loop : -2.43 (0.27), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 50 HIS 0.004 0.002 HIS L 100 PHE 0.010 0.001 PHE H 98 TYR 0.017 0.002 TYR B 62 ARG 0.004 0.001 ARG B 105 Details of bonding type rmsd hydrogen bonds : bond 0.04232 ( 211) hydrogen bonds : angle 4.87340 ( 582) SS BOND : bond 0.00313 ( 1) SS BOND : angle 1.51952 ( 2) covalent geometry : bond 0.00527 ( 5740) covalent geometry : angle 0.60460 ( 7813) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1478 Ramachandran restraints generated. 739 Oldfield, 0 Emsley, 739 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 108 time to evaluate : 0.598 Fit side-chains REVERT: L 72 ILE cc_start: 0.9074 (mt) cc_final: 0.8647 (pt) REVERT: L 75 LYS cc_start: 0.8102 (mtmt) cc_final: 0.7807 (mtmm) REVERT: H 21 LEU cc_start: 0.7153 (OUTLIER) cc_final: 0.6475 (tm) REVERT: H 105 ASP cc_start: 0.7700 (OUTLIER) cc_final: 0.7337 (t0) REVERT: A 81 ASP cc_start: 0.8233 (m-30) cc_final: 0.7262 (p0) REVERT: A 127 GLN cc_start: 0.9090 (mp10) cc_final: 0.8784 (mm-40) REVERT: b 2 LYS cc_start: 0.8530 (tttt) cc_final: 0.7818 (mmtt) REVERT: b 24 ARG cc_start: 0.9042 (mtp180) cc_final: 0.6463 (tpt170) REVERT: b 60 LYS cc_start: 0.8959 (pttm) cc_final: 0.8637 (ptpp) REVERT: b 123 ASP cc_start: 0.9224 (t70) cc_final: 0.8927 (t0) REVERT: B 47 ARG cc_start: 0.8435 (ptp90) cc_final: 0.8137 (ptp-110) REVERT: B 61 ASN cc_start: 0.8676 (m-40) cc_final: 0.8267 (m-40) REVERT: C 2 LYS cc_start: 0.8468 (tttt) cc_final: 0.6300 (mmtt) REVERT: C 61 ASN cc_start: 0.7966 (m-40) cc_final: 0.7751 (m110) REVERT: C 87 GLN cc_start: 0.9228 (mt0) cc_final: 0.8993 (mt0) REVERT: C 121 LEU cc_start: 0.8837 (mm) cc_final: 0.8532 (mt) REVERT: C 122 ILE cc_start: 0.8676 (pt) cc_final: 0.8046 (mm) outliers start: 19 outliers final: 15 residues processed: 123 average time/residue: 0.1984 time to fit residues: 31.3408 Evaluate side-chains 125 residues out of total 616 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 108 time to evaluate : 0.571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 8 VAL Chi-restraints excluded: chain H residue 21 LEU Chi-restraints excluded: chain H residue 24 SER Chi-restraints excluded: chain H residue 66 THR Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain H residue 118 THR Chi-restraints excluded: chain A residue 4 GLU Chi-restraints excluded: chain A residue 85 THR Chi-restraints excluded: chain A residue 93 THR Chi-restraints excluded: chain b residue 7 THR Chi-restraints excluded: chain b residue 8 LEU Chi-restraints excluded: chain b residue 49 THR Chi-restraints excluded: chain b residue 75 THR Chi-restraints excluded: chain B residue 20 VAL Chi-restraints excluded: chain B residue 49 THR Chi-restraints excluded: chain B residue 128 LEU Chi-restraints excluded: chain C residue 51 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 41 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 22 optimal weight: 0.4980 chunk 3 optimal weight: 10.0000 chunk 35 optimal weight: 0.6980 chunk 39 optimal weight: 7.9990 chunk 64 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 overall best weight: 1.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3504 r_free = 0.3504 target = 0.126354 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.096018 restraints weight = 7464.998| |-----------------------------------------------------------------------------| r_work (start): 0.3119 rms_B_bonded: 2.55 r_work: 0.3002 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.2871 rms_B_bonded: 4.48 restraints_weight: 0.2500 r_work (final): 0.2871 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.4748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5741 Z= 0.113 Angle : 0.529 7.388 7815 Z= 0.282 Chirality : 0.046 0.162 921 Planarity : 0.004 0.042 1021 Dihedral : 4.256 25.497 808 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 3.25 % Allowed : 16.40 % Favored : 80.36 % 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: -1.47 (0.29), residues: 739 helix: 0.46 (0.56), residues: 96 sheet: -0.01 (0.30), residues: 306 loop : -2.40 (0.27), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 113 HIS 0.004 0.001 HIS H 108 PHE 0.006 0.001 PHE L 49 TYR 0.010 0.001 TYR B 62 ARG 0.003 0.000 ARG L 26 Details of bonding type rmsd hydrogen bonds : bond 0.03634 ( 211) hydrogen bonds : angle 4.56312 ( 582) SS BOND : bond 0.00111 ( 1) SS BOND : angle 0.76478 ( 2) covalent geometry : bond 0.00251 ( 5740) covalent geometry : angle 0.52905 ( 7813) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3417.04 seconds wall clock time: 59 minutes 45.50 seconds (3585.50 seconds total)