Starting phenix.real_space_refine on Sun Mar 10 20:25:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjl_23877/03_2024/7mjl_23877.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjl_23877/03_2024/7mjl_23877.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjl_23877/03_2024/7mjl_23877.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjl_23877/03_2024/7mjl_23877.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjl_23877/03_2024/7mjl_23877.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mjl_23877/03_2024/7mjl_23877.pdb" } resolution = 2.95 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.024 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 19 5.16 5 C 3037 2.51 5 N 793 2.21 5 O 939 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 369": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 428": "OD1" <-> "OD2" Residue "A ASP 467": "OD1" <-> "OD2" Residue "H PHE 27": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 88": "OE1" <-> "OE2" Residue "H TYR 149": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L TYR 36": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "L GLU 81": "OE1" <-> "OE2" Residue "L ASP 82": "OD1" <-> "OD2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 123": "OE1" <-> "OE2" Residue "L GLU 143": "OE1" <-> "OE2" Residue "L ASP 170": "OD1" <-> "OD2" Residue "L TYR 186": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 209": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 4788 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1564 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 1564 Classifications: {'peptide': 197} Link IDs: {'PTRANS': 11, 'TRANS': 185} Chain: "H" Number of atoms: 1585 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1585 Classifications: {'peptide': 211} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 199} Chain breaks: 1 Chain: "L" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1625 Classifications: {'peptide': 213} Link IDs: {'PCIS': 2, 'PTRANS': 10, 'TRANS': 200} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 3.22, per 1000 atoms: 0.67 Number of scatterers: 4788 At special positions: 0 Unit cell: (75, 62, 129, 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 19 16.00 O 939 8.00 N 793 7.00 C 3037 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS H 144 " - pdb=" SG CYS H 200 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A1301 " - " ASN A 343 " Time building additional restraints: 1.69 Conformation dependent library (CDL) restraints added in 889.0 milliseconds 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 11 helices and 14 sheets defined 9.5% alpha, 42.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.873A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 384 through 389 removed outlier: 4.098A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.697A pdb=" N ASN H 32 " --> pdb=" O VAL H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'H' and resid 86 through 90 removed outlier: 3.734A pdb=" N THR H 90 " --> pdb=" O ALA H 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.652A pdb=" N ASP L 82 " --> pdb=" O GLN L 79 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N VAL L 83 " --> pdb=" O ALA L 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'L' and resid 79 through 83' Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.641A pdb=" N LYS L 126 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.613A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.594A pdb=" N THR H 77 " --> pdb=" O HIS H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 11 through 12 removed outlier: 4.318A pdb=" N TYR H 33 " --> pdb=" O GLY H 98 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.422A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.606A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.921A pdb=" N TYR H 106 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.135A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 124 through 128 removed outlier: 4.135A pdb=" N GLY H 143 " --> pdb=" O LEU H 128 " (cutoff:3.500A) removed outlier: 6.017A pdb=" N TYR H 180 " --> pdb=" O ASP H 148 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 155 through 158 removed outlier: 4.055A pdb=" N TYR H 198 " --> pdb=" O VAL H 215 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N LYS H 213 " --> pdb=" O CYS H 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.632A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.390A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.670A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.390A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 114 through 118 removed outlier: 5.437A pdb=" N SER L 131 " --> pdb=" O LEU L 181 " (cutoff:3.500A) removed outlier: 7.403A pdb=" N LEU L 181 " --> pdb=" O SER L 131 " (cutoff:3.500A) removed outlier: 5.606A pdb=" N VAL L 133 " --> pdb=" O LEU L 179 " (cutoff:3.500A) removed outlier: 7.298A pdb=" N LEU L 179 " --> pdb=" O VAL L 133 " (cutoff:3.500A) removed outlier: 5.490A pdb=" N LEU L 135 " --> pdb=" O SER L 177 " (cutoff:3.500A) removed outlier: 7.289A pdb=" N SER L 177 " --> pdb=" O LEU L 135 " (cutoff:3.500A) removed outlier: 5.235A pdb=" N ASN L 137 " --> pdb=" O LEU L 175 " (cutoff:3.500A) removed outlier: 7.248A pdb=" N LEU L 175 " --> pdb=" O ASN L 137 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 145 through 150 181 hydrogen bonds defined for protein. 453 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: 1.40 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1500 1.34 - 1.46: 1168 1.46 - 1.58: 2219 1.58 - 1.69: 0 1.69 - 1.81: 22 Bond restraints: 4909 Sorted by residual: bond pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.29e-02 6.01e+03 5.98e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.438 -0.032 2.00e-02 2.50e+03 2.60e+00 bond pdb=" C LYS H 205 " pdb=" N PRO H 206 " ideal model delta sigma weight residual 1.336 1.355 -0.019 1.20e-02 6.94e+03 2.59e+00 bond pdb=" CB ASN H 73 " pdb=" CG ASN H 73 " ideal model delta sigma weight residual 1.516 1.552 -0.036 2.50e-02 1.60e+03 2.05e+00 bond pdb=" C SER L 94 " pdb=" N PRO L 95 " ideal model delta sigma weight residual 1.334 1.366 -0.032 2.34e-02 1.83e+03 1.87e+00 ... (remaining 4904 not shown) Histogram of bond angle deviations from ideal: 98.66 - 105.73: 124 105.73 - 112.80: 2520 112.80 - 119.87: 1623 119.87 - 126.94: 2351 126.94 - 134.01: 64 Bond angle restraints: 6682 Sorted by residual: angle pdb=" C GLY H 100 " pdb=" N ASP H 101 " pdb=" CA ASP H 101 " ideal model delta sigma weight residual 121.54 129.87 -8.33 1.91e+00 2.74e-01 1.90e+01 angle pdb=" C TRP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 128.33 -6.79 1.91e+00 2.74e-01 1.26e+01 angle pdb=" C PHE A 515 " pdb=" N GLU A 516 " pdb=" CA GLU A 516 " ideal model delta sigma weight residual 122.94 117.62 5.32 1.50e+00 4.44e-01 1.26e+01 angle pdb=" CA ASP H 101 " pdb=" CB ASP H 101 " pdb=" CG ASP H 101 " ideal model delta sigma weight residual 112.60 115.97 -3.37 1.00e+00 1.00e+00 1.14e+01 angle pdb=" CA LYS H 210 " pdb=" CB LYS H 210 " pdb=" CG LYS H 210 " ideal model delta sigma weight residual 114.10 120.52 -6.42 2.00e+00 2.50e-01 1.03e+01 ... (remaining 6677 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.53: 2713 16.53 - 33.06: 151 33.06 - 49.59: 38 49.59 - 66.12: 11 66.12 - 82.65: 8 Dihedral angle restraints: 2921 sinusoidal: 1124 harmonic: 1797 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 167.49 -74.49 1 1.00e+01 1.00e-02 7.03e+01 dihedral pdb=" CB CYS H 144 " pdb=" SG CYS H 144 " pdb=" SG CYS H 200 " pdb=" CB CYS H 200 " ideal model delta sinusoidal sigma weight residual 93.00 144.05 -51.05 1 1.00e+01 1.00e-02 3.56e+01 dihedral pdb=" CA HIS H 72 " pdb=" C HIS H 72 " pdb=" N ASN H 73 " pdb=" CA ASN H 73 " ideal model delta harmonic sigma weight residual 180.00 -157.47 -22.53 0 5.00e+00 4.00e-02 2.03e+01 ... (remaining 2918 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 506 0.047 - 0.094: 159 0.094 - 0.142: 61 0.142 - 0.189: 9 0.189 - 0.236: 2 Chirality restraints: 737 Sorted by residual: chirality pdb=" CA ASP H 101 " pdb=" N ASP H 101 " pdb=" C ASP H 101 " pdb=" CB ASP H 101 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CB ILE A 332 " pdb=" CA ILE A 332 " pdb=" CG1 ILE A 332 " pdb=" CG2 ILE A 332 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CB ILE L 117 " pdb=" CA ILE L 117 " pdb=" CG1 ILE L 117 " pdb=" CG2 ILE L 117 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.17e-01 ... (remaining 734 not shown) Planarity restraints: 859 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.036 5.00e-02 4.00e+02 5.48e-02 4.80e+00 pdb=" N PRO A 479 " -0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU H 152 " -0.034 5.00e-02 4.00e+02 5.15e-02 4.24e+00 pdb=" N PRO H 153 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO H 153 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO H 153 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 60 " 0.009 2.00e-02 2.50e+03 1.86e-02 3.47e+00 pdb=" CG ASP L 60 " -0.032 2.00e-02 2.50e+03 pdb=" OD1 ASP L 60 " 0.012 2.00e-02 2.50e+03 pdb=" OD2 ASP L 60 " 0.011 2.00e-02 2.50e+03 ... (remaining 856 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 1635 2.86 - 3.37: 3870 3.37 - 3.88: 8010 3.88 - 4.39: 9038 4.39 - 4.90: 15985 Nonbonded interactions: 38538 Sorted by model distance: nonbonded pdb=" O TRP A 353 " pdb=" NH1 ARG A 466 " model vdw 2.351 2.520 nonbonded pdb=" OG SER A 366 " pdb=" OD1 ASN A 388 " model vdw 2.354 2.440 nonbonded pdb=" OD2 ASP A 420 " pdb=" OG SER H 56 " model vdw 2.359 2.440 nonbonded pdb=" OH TYR A 453 " pdb=" OH TYR H 102 " model vdw 2.371 2.440 nonbonded pdb=" OG SER H 207 " pdb=" OG1 THR H 209 " model vdw 2.404 2.440 ... (remaining 38533 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.270 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: 13.070 Check model and map are aligned: 0.060 Set scattering table: 0.050 Process input model: 17.490 Find NCS groups from input model: 0.160 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:12.260 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 4909 Z= 0.325 Angle : 0.818 8.326 6682 Z= 0.444 Chirality : 0.054 0.236 737 Planarity : 0.006 0.055 858 Dihedral : 12.247 82.651 1757 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.85 (0.32), residues: 613 helix: -4.72 (0.22), residues: 37 sheet: 0.46 (0.32), residues: 243 loop : -0.82 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 436 HIS 0.005 0.002 HIS H 72 PHE 0.015 0.002 PHE L 71 TYR 0.025 0.002 TYR A 495 ARG 0.006 0.001 ARG H 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.493 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 516 GLU cc_start: 0.8034 (pp20) cc_final: 0.7555 (pp20) REVERT: A 528 LYS cc_start: 0.5794 (tttm) cc_final: 0.4720 (pptt) REVERT: L 158 ASN cc_start: 0.7795 (m110) cc_final: 0.7591 (m110) REVERT: L 167 ASP cc_start: 0.8609 (t0) cc_final: 0.8273 (t0) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 1.3259 time to fit residues: 123.4240 Evaluate side-chains 61 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 61 time to evaluate : 0.584 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 0.8980 chunk 46 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 47 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 29 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 201 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8466 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 4909 Z= 0.175 Angle : 0.526 6.599 6682 Z= 0.273 Chirality : 0.043 0.141 737 Planarity : 0.005 0.052 858 Dihedral : 5.008 40.664 699 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.38 % Allowed : 10.17 % Favored : 89.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.33), residues: 613 helix: -4.68 (0.49), residues: 20 sheet: 0.59 (0.33), residues: 244 loop : -0.40 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 158 HIS 0.003 0.001 HIS H 72 PHE 0.007 0.001 PHE L 71 TYR 0.015 0.001 TYR A 495 ARG 0.011 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.554 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8738 (m-30) cc_final: 0.8466 (m-30) REVERT: A 516 GLU cc_start: 0.7734 (pp20) cc_final: 0.7304 (pp20) REVERT: A 528 LYS cc_start: 0.5786 (tttm) cc_final: 0.4745 (pptt) REVERT: H 3 GLN cc_start: 0.8016 (mm110) cc_final: 0.7777 (mm110) REVERT: L 167 ASP cc_start: 0.8751 (t0) cc_final: 0.8334 (t0) outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 1.3374 time to fit residues: 104.0901 Evaluate side-chains 63 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 0.2980 chunk 17 optimal weight: 0.0050 chunk 46 optimal weight: 5.9990 chunk 37 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.4980 chunk 44 optimal weight: 2.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN H 109 GLN L 155 GLN L 158 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8460 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 4909 Z= 0.159 Angle : 0.491 6.643 6682 Z= 0.254 Chirality : 0.042 0.135 737 Planarity : 0.004 0.050 858 Dihedral : 4.346 22.115 699 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 6.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 0.75 % Allowed : 12.24 % Favored : 87.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.34), residues: 613 helix: -4.35 (0.75), residues: 19 sheet: 0.75 (0.33), residues: 244 loop : -0.20 (0.33), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 158 HIS 0.003 0.001 HIS H 72 PHE 0.007 0.001 PHE L 71 TYR 0.015 0.001 TYR H 79 ARG 0.011 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8739 (m-30) cc_final: 0.8403 (m-30) REVERT: A 516 GLU cc_start: 0.7661 (pp20) cc_final: 0.7177 (pp20) REVERT: A 528 LYS cc_start: 0.5471 (tttm) cc_final: 0.4858 (pptt) REVERT: L 167 ASP cc_start: 0.8715 (t0) cc_final: 0.8270 (t0) REVERT: L 170 ASP cc_start: 0.8603 (p0) cc_final: 0.8338 (p0) outliers start: 4 outliers final: 2 residues processed: 75 average time/residue: 1.2909 time to fit residues: 100.5405 Evaluate side-chains 65 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 63 time to evaluate : 0.569 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.9980 chunk 49 optimal weight: 1.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN H 109 GLN L 137 ASN L 152 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.1817 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4909 Z= 0.322 Angle : 0.553 7.020 6682 Z= 0.285 Chirality : 0.043 0.131 737 Planarity : 0.004 0.052 858 Dihedral : 4.663 23.761 699 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.69 % Allowed : 12.62 % Favored : 85.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.34), residues: 613 helix: -4.24 (0.99), residues: 18 sheet: 0.71 (0.33), residues: 246 loop : -0.18 (0.34), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.003 0.001 HIS H 72 PHE 0.009 0.001 PHE L 71 TYR 0.019 0.001 TYR L 140 ARG 0.005 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 63 time to evaluate : 0.589 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8753 (m-30) cc_final: 0.8340 (m-30) REVERT: A 516 GLU cc_start: 0.7676 (pp20) cc_final: 0.7097 (pp20) REVERT: A 518 LEU cc_start: 0.8860 (mt) cc_final: 0.8582 (mp) REVERT: A 528 LYS cc_start: 0.5514 (tttm) cc_final: 0.4733 (pptt) REVERT: H 3 GLN cc_start: 0.8221 (mp10) cc_final: 0.7957 (mp10) REVERT: H 147 LYS cc_start: 0.8962 (OUTLIER) cc_final: 0.8759 (ttmm) REVERT: H 205 LYS cc_start: 0.8814 (mmmt) cc_final: 0.8277 (tptp) REVERT: L 167 ASP cc_start: 0.8815 (t0) cc_final: 0.8372 (t0) outliers start: 9 outliers final: 4 residues processed: 65 average time/residue: 1.2416 time to fit residues: 84.0966 Evaluate side-chains 62 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.556 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 147 LYS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 50 optimal weight: 4.9990 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 19 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN L 137 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.026 4909 Z= 0.339 Angle : 0.546 6.802 6682 Z= 0.284 Chirality : 0.043 0.134 737 Planarity : 0.004 0.049 858 Dihedral : 4.686 24.694 699 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.45 % Allowed : 14.12 % Favored : 83.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.35), residues: 613 helix: -4.26 (0.95), residues: 18 sheet: 0.73 (0.34), residues: 243 loop : -0.09 (0.35), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.008 0.001 PHE L 71 TYR 0.015 0.002 TYR L 140 ARG 0.005 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8786 (m-30) cc_final: 0.8364 (m-30) REVERT: A 462 LYS cc_start: 0.9089 (OUTLIER) cc_final: 0.8601 (mttm) REVERT: A 516 GLU cc_start: 0.7663 (OUTLIER) cc_final: 0.7056 (pp20) REVERT: A 528 LYS cc_start: 0.5590 (tttm) cc_final: 0.4805 (pptt) REVERT: H 3 GLN cc_start: 0.8244 (mp10) cc_final: 0.7929 (mp10) REVERT: L 167 ASP cc_start: 0.8860 (t0) cc_final: 0.8435 (t0) outliers start: 13 outliers final: 6 residues processed: 66 average time/residue: 1.1944 time to fit residues: 82.1972 Evaluate side-chains 66 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 14 optimal weight: 0.9980 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 0.8980 chunk 56 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 414 GLN H 109 GLN L 137 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8504 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 4909 Z= 0.232 Angle : 0.520 6.688 6682 Z= 0.266 Chirality : 0.043 0.134 737 Planarity : 0.004 0.048 858 Dihedral : 4.467 20.253 699 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.26 % Allowed : 15.07 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.35), residues: 613 helix: -4.47 (0.51), residues: 33 sheet: 0.89 (0.34), residues: 241 loop : -0.19 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 158 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE L 71 TYR 0.013 0.001 TYR L 173 ARG 0.004 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 62 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8780 (m-30) cc_final: 0.8358 (m-30) REVERT: A 462 LYS cc_start: 0.9072 (OUTLIER) cc_final: 0.8571 (mttm) REVERT: A 516 GLU cc_start: 0.7569 (OUTLIER) cc_final: 0.7280 (pp20) REVERT: A 528 LYS cc_start: 0.5584 (tttm) cc_final: 0.4859 (pptt) REVERT: H 3 GLN cc_start: 0.8262 (mp10) cc_final: 0.7932 (mp10) REVERT: H 88 GLU cc_start: 0.8691 (pm20) cc_final: 0.8453 (pm20) REVERT: H 205 LYS cc_start: 0.8789 (mmmt) cc_final: 0.8202 (tptp) REVERT: L 167 ASP cc_start: 0.8851 (t0) cc_final: 0.8232 (t0) outliers start: 12 outliers final: 7 residues processed: 65 average time/residue: 1.2992 time to fit residues: 87.8036 Evaluate side-chains 66 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 0.6980 chunk 49 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 chunk 17 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8493 moved from start: 0.2059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4909 Z= 0.203 Angle : 0.496 6.681 6682 Z= 0.256 Chirality : 0.042 0.133 737 Planarity : 0.004 0.047 858 Dihedral : 4.259 20.326 699 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.26 % Allowed : 15.44 % Favored : 82.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.35), residues: 613 helix: -4.43 (0.50), residues: 33 sheet: 1.00 (0.34), residues: 241 loop : -0.17 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 158 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE L 98 TYR 0.012 0.001 TYR L 173 ARG 0.003 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 59 time to evaluate : 0.563 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8785 (m-30) cc_final: 0.8362 (m-30) REVERT: A 462 LYS cc_start: 0.9053 (OUTLIER) cc_final: 0.8552 (mttm) REVERT: A 516 GLU cc_start: 0.7631 (OUTLIER) cc_final: 0.7066 (pp20) REVERT: A 518 LEU cc_start: 0.8838 (mt) cc_final: 0.8637 (mp) REVERT: A 528 LYS cc_start: 0.5602 (tttm) cc_final: 0.4878 (pptt) REVERT: H 3 GLN cc_start: 0.8254 (mp10) cc_final: 0.7923 (mp10) REVERT: L 142 ARG cc_start: 0.8972 (tpp80) cc_final: 0.8544 (ttt-90) REVERT: L 167 ASP cc_start: 0.8777 (t0) cc_final: 0.8422 (t0) outliers start: 12 outliers final: 6 residues processed: 65 average time/residue: 1.2423 time to fit residues: 84.2117 Evaluate side-chains 65 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 57 time to evaluate : 0.539 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 29 optimal weight: 0.9990 chunk 5 optimal weight: 3.9990 chunk 46 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 56 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.6980 chunk 32 optimal weight: 0.7980 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2130 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 4909 Z= 0.296 Angle : 0.533 8.196 6682 Z= 0.276 Chirality : 0.043 0.133 737 Planarity : 0.004 0.049 858 Dihedral : 4.487 21.224 699 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.59 % Favored : 96.41 % Rotamer: Outliers : 2.26 % Allowed : 15.82 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.00 (0.35), residues: 613 helix: -4.46 (0.52), residues: 33 sheet: 0.99 (0.34), residues: 240 loop : -0.21 (0.35), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 47 HIS 0.003 0.001 HIS A 519 PHE 0.007 0.001 PHE L 71 TYR 0.013 0.001 TYR L 173 ARG 0.004 0.001 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 64 time to evaluate : 0.555 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8794 (m-30) cc_final: 0.8344 (m-30) REVERT: A 430 THR cc_start: 0.9303 (OUTLIER) cc_final: 0.8996 (p) REVERT: A 462 LYS cc_start: 0.9048 (OUTLIER) cc_final: 0.8553 (mttm) REVERT: A 516 GLU cc_start: 0.7673 (OUTLIER) cc_final: 0.7086 (pp20) REVERT: A 518 LEU cc_start: 0.8870 (mt) cc_final: 0.8648 (mp) REVERT: A 528 LYS cc_start: 0.5609 (tttm) cc_final: 0.4821 (pptt) REVERT: H 3 GLN cc_start: 0.8272 (mp10) cc_final: 0.7907 (mp10) REVERT: H 205 LYS cc_start: 0.8784 (mmmt) cc_final: 0.8333 (tptp) REVERT: L 167 ASP cc_start: 0.8865 (t0) cc_final: 0.8270 (t0) outliers start: 12 outliers final: 7 residues processed: 68 average time/residue: 1.2851 time to fit residues: 90.9931 Evaluate side-chains 66 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 56 time to evaluate : 0.589 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain H residue 105 ASP Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 2.9990 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 1.9990 chunk 27 optimal weight: 0.8980 chunk 40 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8499 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4909 Z= 0.231 Angle : 0.528 6.944 6682 Z= 0.275 Chirality : 0.043 0.162 737 Planarity : 0.004 0.046 858 Dihedral : 4.331 20.509 699 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 2.07 % Allowed : 16.57 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.35), residues: 613 helix: -4.45 (0.50), residues: 33 sheet: 0.99 (0.34), residues: 241 loop : -0.19 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE L 98 TYR 0.013 0.001 TYR L 173 ARG 0.004 0.000 ARG H 86 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 57 time to evaluate : 0.552 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8791 (m-30) cc_final: 0.8344 (m-30) REVERT: A 430 THR cc_start: 0.9299 (OUTLIER) cc_final: 0.8979 (p) REVERT: A 462 LYS cc_start: 0.9050 (OUTLIER) cc_final: 0.8536 (mttm) REVERT: A 516 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7092 (pp20) REVERT: A 528 LYS cc_start: 0.5605 (tttm) cc_final: 0.4838 (pptt) REVERT: H 3 GLN cc_start: 0.8275 (mp10) cc_final: 0.7910 (mp10) REVERT: H 205 LYS cc_start: 0.8759 (mmmt) cc_final: 0.8256 (tptp) REVERT: L 142 ARG cc_start: 0.8960 (tpp80) cc_final: 0.8580 (ttt-90) REVERT: L 167 ASP cc_start: 0.8806 (t0) cc_final: 0.8433 (t0) outliers start: 11 outliers final: 6 residues processed: 63 average time/residue: 1.1935 time to fit residues: 78.5307 Evaluate side-chains 68 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 59 time to evaluate : 0.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 427 ASP Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain A residue 516 GLU Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Chi-restraints excluded: chain L residue 105 GLU Chi-restraints excluded: chain L residue 161 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 0.4980 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 37 optimal weight: 0.5980 chunk 29 optimal weight: 0.3980 chunk 38 optimal weight: 5.9990 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 44 optimal weight: 0.0470 chunk 7 optimal weight: 0.7980 chunk 13 optimal weight: 0.9980 overall best weight: 0.4678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.2271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4909 Z= 0.176 Angle : 0.517 7.484 6682 Z= 0.266 Chirality : 0.043 0.136 737 Planarity : 0.004 0.045 858 Dihedral : 4.113 19.981 699 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.51 % Allowed : 17.14 % Favored : 81.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.10 (0.35), residues: 613 helix: -4.38 (0.49), residues: 33 sheet: 1.12 (0.34), residues: 242 loop : -0.20 (0.35), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS A 519 PHE 0.006 0.001 PHE L 98 TYR 0.013 0.001 TYR L 173 ARG 0.004 0.000 ARG H 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1226 Ramachandran restraints generated. 613 Oldfield, 0 Emsley, 613 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 66 time to evaluate : 0.513 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 420 ASP cc_start: 0.8774 (m-30) cc_final: 0.8355 (m-30) REVERT: A 430 THR cc_start: 0.9288 (OUTLIER) cc_final: 0.8952 (p) REVERT: A 462 LYS cc_start: 0.8999 (OUTLIER) cc_final: 0.8476 (mttm) REVERT: A 528 LYS cc_start: 0.5602 (tttm) cc_final: 0.4895 (pptt) REVERT: H 3 GLN cc_start: 0.8262 (mp10) cc_final: 0.7904 (mp10) REVERT: H 205 LYS cc_start: 0.8730 (mmmt) cc_final: 0.8163 (tptp) REVERT: L 142 ARG cc_start: 0.8950 (tpp80) cc_final: 0.8586 (ttt-90) REVERT: L 167 ASP cc_start: 0.8768 (t0) cc_final: 0.8155 (t0) outliers start: 8 outliers final: 3 residues processed: 69 average time/residue: 1.1495 time to fit residues: 82.8066 Evaluate side-chains 64 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 59 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 367 VAL Chi-restraints excluded: chain A residue 430 THR Chi-restraints excluded: chain A residue 462 LYS Chi-restraints excluded: chain H residue 72 HIS Chi-restraints excluded: chain L residue 10 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 2 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 3.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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 = 0.3079 r_free = 0.3079 target = 0.062834 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.052387 restraints weight = 12605.579| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 2.90 r_work: 0.2714 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work (final): 0.2714 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 4909 Z= 0.258 Angle : 0.532 6.658 6682 Z= 0.276 Chirality : 0.044 0.154 737 Planarity : 0.004 0.046 858 Dihedral : 4.344 20.949 699 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 1.32 % Allowed : 16.95 % Favored : 81.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.35), residues: 613 helix: -4.37 (0.51), residues: 33 sheet: 1.04 (0.34), residues: 241 loop : -0.18 (0.35), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS A 519 PHE 0.006 0.001 PHE L 71 TYR 0.016 0.001 TYR H 79 ARG 0.006 0.001 ARG H 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2174.57 seconds wall clock time: 39 minutes 26.29 seconds (2366.29 seconds total)