Starting phenix.real_space_refine on Mon Sep 23 17:22:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/09_2024/8dm4_27526.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/09_2024/8dm4_27526.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.45 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/09_2024/8dm4_27526.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/09_2024/8dm4_27526.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/09_2024/8dm4_27526.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dm4_27526/09_2024/8dm4_27526.cif" } resolution = 2.45 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.017 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 18 5.16 5 C 2563 2.51 5 N 653 2.21 5 O 784 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4018 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 2096 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2096 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 11, 'TRANS': 245} Chain breaks: 3 Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 976 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 4, 'TRANS': 123} Chain: "L" Number of atoms: 862 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 862 Classifications: {'peptide': 112} Link IDs: {'PCIS': 2, 'PTRANS': 6, 'TRANS': 103} Chain: "B" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Chain: "A" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 56 Unusual residues: {'NAG': 4} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 4.15, per 1000 atoms: 1.03 Number of scatterers: 4018 At special positions: 0 Unit cell: (101, 61, 97, 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 18 16.00 O 784 8.00 N 653 7.00 C 2563 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.04 Simple disulfide: pdb=" SG CYS H 41 " - pdb=" SG CYS H 115 " distance=2.03 Simple disulfide: pdb=" SG CYS L 43 " - pdb=" SG CYS L 113 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " NAG-ASN " NAG A1301 " - " ASN A 61 " " NAG A1302 " - " ASN A 165 " " NAG A1303 " - " ASN A 234 " " NAG A1304 " - " ASN A 282 " " NAG B 1 " - " ASN A 122 " Time building additional restraints: 0.94 Conformation dependent library (CDL) restraints added in 460.7 milliseconds 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 924 Finding SS restraints... Secondary structure from input PDB file: 2 helices and 10 sheets defined 1.6% alpha, 47.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.58 Creating SS restraints... Processing helix chain 'H' and resid 47 through 49 No H-bonds generated for 'chain 'H' and resid 47 through 49' Processing helix chain 'H' and resid 106 through 110 removed outlier: 4.019A pdb=" N THR H 110 " --> pdb=" O SER H 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 20 through 30 removed outlier: 7.905A pdb=" N ASN A 61 " --> pdb=" O TYR A 269 " (cutoff:3.500A) removed outlier: 5.706A pdb=" N TYR A 269 " --> pdb=" O ASN A 61 " (cutoff:3.500A) removed outlier: 6.072A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 47 through 55 removed outlier: 3.872A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 Processing sheet with id=AA4, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.766A pdb=" N GLY A 103 " --> pdb=" O LEU A 241 " (cutoff:3.500A) removed outlier: 6.396A pdb=" N ALA A 243 " --> pdb=" O ILE A 101 " (cutoff:3.500A) removed outlier: 6.283A pdb=" N ILE A 101 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 5.787A pdb=" N ARG A 102 " --> pdb=" O ASN A 121 " (cutoff:3.500A) removed outlier: 7.155A pdb=" N GLU A 132 " --> pdb=" O CYS A 166 " (cutoff:3.500A) removed outlier: 7.190A pdb=" N CYS A 166 " --> pdb=" O GLU A 132 " (cutoff:3.500A) removed outlier: 7.532A pdb=" N GLN A 134 " --> pdb=" O ASN A 164 " (cutoff:3.500A) removed outlier: 8.842A pdb=" N ASN A 164 " --> pdb=" O GLN A 134 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 22 through 25 removed outlier: 3.711A pdb=" N VAL H 37 " --> pdb=" O LEU H 102 " (cutoff:3.500A) removed outlier: 3.827A pdb=" N LEU H 102 " --> pdb=" O VAL H 37 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) removed outlier: 6.643A pdb=" N MET H 53 " --> pdb=" O GLY H 69 " (cutoff:3.500A) removed outlier: 4.515A pdb=" N GLY H 69 " --> pdb=" O MET H 53 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 55 " --> pdb=" O MET H 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 29 through 30 removed outlier: 6.409A pdb=" N GLU H 29 " --> pdb=" O THR H 144 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 121 through 123 Processing sheet with id=AA9, first strand: chain 'L' and resid 24 through 27 Processing sheet with id=AB1, first strand: chain 'L' and resid 30 through 32 removed outlier: 4.284A pdb=" N ASP L 130 " --> pdb=" O SER L 31 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLN L 62 " --> pdb=" O LEU L 71 " (cutoff:3.500A) removed outlier: 5.713A pdb=" N LEU L 71 " --> pdb=" O GLN L 62 " (cutoff:3.500A) 159 hydrogen bonds defined for protein. 399 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: 1.16 Time building geometry restraints manager: 1.11 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: 1249 1.34 - 1.46: 1064 1.46 - 1.58: 1777 1.58 - 1.70: 0 1.70 - 1.82: 27 Bond restraints: 4117 Sorted by residual: bond pdb=" C1 NAG A1302 " pdb=" O5 NAG A1302 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 3.94e+00 bond pdb=" C1 NAG A1304 " pdb=" O5 NAG A1304 " ideal model delta sigma weight residual 1.406 1.445 -0.039 2.00e-02 2.50e+03 3.76e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.442 -0.036 2.00e-02 2.50e+03 3.16e+00 bond pdb=" C1 NAG A1303 " pdb=" O5 NAG A1303 " ideal model delta sigma weight residual 1.406 1.437 -0.031 2.00e-02 2.50e+03 2.43e+00 bond pdb=" C1 NAG A1301 " pdb=" O5 NAG A1301 " ideal model delta sigma weight residual 1.406 1.436 -0.030 2.00e-02 2.50e+03 2.18e+00 ... (remaining 4112 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.08: 5350 2.08 - 4.16: 220 4.16 - 6.23: 18 6.23 - 8.31: 3 8.31 - 10.39: 3 Bond angle restraints: 5594 Sorted by residual: angle pdb=" C ILE A 197 " pdb=" N ASP A 198 " pdb=" CA ASP A 198 " ideal model delta sigma weight residual 121.54 131.93 -10.39 1.91e+00 2.74e-01 2.96e+01 angle pdb=" C LEU A 141 " pdb=" N ASP A 142 " pdb=" CA ASP A 142 " ideal model delta sigma weight residual 122.93 118.21 4.72 1.45e+00 4.76e-01 1.06e+01 angle pdb=" CA CYS A 131 " pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " ideal model delta sigma weight residual 114.40 121.47 -7.07 2.30e+00 1.89e-01 9.45e+00 angle pdb=" CA ASP A 198 " pdb=" CB ASP A 198 " pdb=" CG ASP A 198 " ideal model delta sigma weight residual 112.60 115.65 -3.05 1.00e+00 1.00e+00 9.29e+00 angle pdb=" N THR L 34 " pdb=" CA THR L 34 " pdb=" C THR L 34 " ideal model delta sigma weight residual 110.35 106.53 3.82 1.38e+00 5.25e-01 7.64e+00 ... (remaining 5589 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.82: 2302 17.82 - 35.63: 148 35.63 - 53.45: 27 53.45 - 71.27: 13 71.27 - 89.09: 4 Dihedral angle restraints: 2494 sinusoidal: 1051 harmonic: 1443 Sorted by residual: dihedral pdb=" CB CYS A 131 " pdb=" SG CYS A 131 " pdb=" SG CYS A 166 " pdb=" CB CYS A 166 " ideal model delta sinusoidal sigma weight residual -86.00 -51.05 -34.95 1 1.00e+01 1.00e-02 1.73e+01 dihedral pdb=" CA VAL H 24 " pdb=" C VAL H 24 " pdb=" N GLU H 25 " pdb=" CA GLU H 25 " ideal model delta harmonic sigma weight residual -180.00 -159.50 -20.50 0 5.00e+00 4.00e-02 1.68e+01 dihedral pdb=" CA VAL A 90 " pdb=" C VAL A 90 " pdb=" N TYR A 91 " pdb=" CA TYR A 91 " ideal model delta harmonic sigma weight residual 180.00 162.24 17.76 0 5.00e+00 4.00e-02 1.26e+01 ... (remaining 2491 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 424 0.051 - 0.102: 159 0.102 - 0.152: 44 0.152 - 0.203: 4 0.203 - 0.254: 3 Chirality restraints: 634 Sorted by residual: chirality pdb=" C1 NAG A1302 " pdb=" ND2 ASN A 165 " pdb=" C2 NAG A1302 " pdb=" O5 NAG A1302 " both_signs ideal model delta sigma weight residual False -2.40 -2.15 -0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB THR L 56 " pdb=" CA THR L 56 " pdb=" OG1 THR L 56 " pdb=" CG2 THR L 56 " both_signs ideal model delta sigma weight residual False 2.55 2.33 0.22 2.00e-01 2.50e+01 1.24e+00 chirality pdb=" CA ASP A 198 " pdb=" N ASP A 198 " pdb=" C ASP A 198 " pdb=" CB ASP A 198 " both_signs ideal model delta sigma weight residual False 2.51 2.29 0.22 2.00e-01 2.50e+01 1.23e+00 ... (remaining 631 not shown) Planarity restraints: 711 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER L 27 " -0.048 5.00e-02 4.00e+02 7.39e-02 8.74e+00 pdb=" N PRO L 28 " 0.128 5.00e-02 4.00e+02 pdb=" CA PRO L 28 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO L 28 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 273 " -0.237 9.50e-02 1.11e+02 1.07e-01 7.74e+00 pdb=" NE ARG A 273 " 0.019 2.00e-02 2.50e+03 pdb=" CZ ARG A 273 " -0.013 2.00e-02 2.50e+03 pdb=" NH1 ARG A 273 " 0.008 2.00e-02 2.50e+03 pdb=" NH2 ARG A 273 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 210 " -0.014 2.00e-02 2.50e+03 2.75e-02 7.57e+00 pdb=" C ILE A 210 " 0.048 2.00e-02 2.50e+03 pdb=" O ILE A 210 " -0.018 2.00e-02 2.50e+03 pdb=" N ASN A 211 " -0.016 2.00e-02 2.50e+03 ... (remaining 708 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 865 2.79 - 3.32: 3144 3.32 - 3.84: 6623 3.84 - 4.37: 7758 4.37 - 4.90: 13925 Nonbonded interactions: 32315 Sorted by model distance: nonbonded pdb=" OG SER L 90 " pdb=" OG1 THR L 97 " model vdw 2.259 3.040 nonbonded pdb=" OD1 ASP H 109 " pdb=" OH TYR H 113 " model vdw 2.279 3.040 nonbonded pdb=" O SER L 45 " pdb=" OG1 THR L 94 " model vdw 2.307 3.040 nonbonded pdb=" OG SER A 247 " pdb=" OH TYR H 46 " model vdw 2.365 3.040 nonbonded pdb=" OH TYR A 37 " pdb=" O LEU A 54 " model vdw 2.368 3.040 ... (remaining 32310 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.430 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: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.290 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 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 0.045 4117 Z= 0.383 Angle : 0.904 10.390 5594 Z= 0.484 Chirality : 0.057 0.254 634 Planarity : 0.008 0.107 706 Dihedral : 13.358 89.087 1558 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 0.23 % Allowed : 0.92 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.55 (0.34), residues: 230 loop : -0.55 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP H 66 HIS 0.003 0.001 HIS A 69 PHE 0.025 0.003 PHE A 175 TYR 0.032 0.003 TYR A 145 ARG 0.016 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.446 Fit side-chains REVERT: A 80 ASP cc_start: 0.6299 (t0) cc_final: 0.6086 (t0) REVERT: A 100 ILE cc_start: 0.8408 (mp) cc_final: 0.8064 (tp) REVERT: H 52 SER cc_start: 0.7982 (m) cc_final: 0.7705 (p) REVERT: H 65 GLU cc_start: 0.6701 (pt0) cc_final: 0.6168 (pm20) REVERT: H 107 SER cc_start: 0.7089 (m) cc_final: 0.6425 (t) REVERT: H 131 TYR cc_start: 0.8106 (t80) cc_final: 0.7868 (t80) REVERT: H 134 MET cc_start: 0.8612 (mtm) cc_final: 0.8405 (mpp) outliers start: 1 outliers final: 0 residues processed: 100 average time/residue: 1.0626 time to fit residues: 110.0613 Evaluate side-chains 72 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 72 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 3.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 0.0970 chunk 19 optimal weight: 0.5980 chunk 37 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 23 GLN A 30 ASN L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.1637 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4117 Z= 0.222 Angle : 0.594 8.324 5594 Z= 0.310 Chirality : 0.045 0.211 634 Planarity : 0.004 0.055 706 Dihedral : 7.344 57.481 665 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.97 % Allowed : 10.30 % Favored : 86.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.77 (0.35), residues: 215 loop : -0.26 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 66 HIS 0.002 0.001 HIS A 69 PHE 0.018 0.002 PHE A 175 TYR 0.015 0.002 TYR A 28 ARG 0.007 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 71 time to evaluate : 0.433 Fit side-chains REVERT: A 80 ASP cc_start: 0.6348 (t0) cc_final: 0.6127 (t0) REVERT: A 169 GLU cc_start: 0.7969 (OUTLIER) cc_final: 0.7001 (tm-30) REVERT: A 173 GLN cc_start: 0.8427 (OUTLIER) cc_final: 0.7933 (mp10) REVERT: H 65 GLU cc_start: 0.7085 (pt0) cc_final: 0.6624 (pm20) REVERT: H 100 MET cc_start: 0.7038 (OUTLIER) cc_final: 0.6774 (tmt) REVERT: H 131 TYR cc_start: 0.8152 (t80) cc_final: 0.7939 (t80) REVERT: H 134 MET cc_start: 0.8661 (mtm) cc_final: 0.8379 (mpp) REVERT: L 132 LYS cc_start: 0.7575 (mmmm) cc_final: 0.7340 (mmmm) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 1.3115 time to fit residues: 97.4791 Evaluate side-chains 74 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.462 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.3980 chunk 43 optimal weight: 3.9990 chunk 47 optimal weight: 1.9990 chunk 38 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 35 optimal weight: 0.0970 chunk 32 optimal weight: 0.6980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 HIS L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.1918 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4117 Z= 0.188 Angle : 0.555 5.294 5594 Z= 0.293 Chirality : 0.044 0.198 634 Planarity : 0.004 0.045 706 Dihedral : 6.716 55.692 665 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 6.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 2.75 % Allowed : 12.59 % Favored : 84.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.45 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.86 (0.35), residues: 213 loop : -0.10 (0.38), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP H 66 HIS 0.005 0.001 HIS A 245 PHE 0.015 0.001 PHE A 175 TYR 0.012 0.001 TYR A 28 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 68 time to evaluate : 0.472 Fit side-chains REVERT: A 80 ASP cc_start: 0.6337 (t0) cc_final: 0.6106 (t0) REVERT: A 169 GLU cc_start: 0.7913 (OUTLIER) cc_final: 0.7003 (tm-30) REVERT: A 173 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7896 (mp10) REVERT: A 177 MET cc_start: 0.7961 (pmt) cc_final: 0.7679 (pmt) REVERT: H 65 GLU cc_start: 0.7205 (pt0) cc_final: 0.6988 (pt0) REVERT: H 78 MET cc_start: 0.6666 (tpp) cc_final: 0.5900 (tpt) REVERT: H 100 MET cc_start: 0.7079 (OUTLIER) cc_final: 0.6832 (ttp) REVERT: H 109 ASP cc_start: 0.7250 (t0) cc_final: 0.7040 (t0) REVERT: H 131 TYR cc_start: 0.8224 (t80) cc_final: 0.7994 (t80) REVERT: H 134 MET cc_start: 0.8638 (mtm) cc_final: 0.8412 (mpp) REVERT: L 117 THR cc_start: 0.8331 (p) cc_final: 0.8089 (p) REVERT: L 132 LYS cc_start: 0.7560 (mmmm) cc_final: 0.7183 (mmmm) outliers start: 12 outliers final: 4 residues processed: 72 average time/residue: 1.2101 time to fit residues: 90.2192 Evaluate side-chains 71 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 64 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 50 VAL Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 43 optimal weight: 0.3980 chunk 46 optimal weight: 2.9990 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 1.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 30 ASN A 245 HIS L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4117 Z= 0.232 Angle : 0.563 5.924 5594 Z= 0.297 Chirality : 0.045 0.200 634 Planarity : 0.004 0.042 706 Dihedral : 6.349 50.924 665 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 3.20 % Allowed : 13.73 % Favored : 83.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.48 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.87 (0.35), residues: 212 loop : -0.07 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.005 0.001 HIS A 245 PHE 0.020 0.002 PHE A 175 TYR 0.012 0.002 TYR A 28 ARG 0.003 0.000 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 68 time to evaluate : 0.409 Fit side-chains REVERT: A 80 ASP cc_start: 0.6333 (t0) cc_final: 0.6113 (t0) REVERT: A 169 GLU cc_start: 0.7928 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: A 173 GLN cc_start: 0.8419 (OUTLIER) cc_final: 0.7887 (mp10) REVERT: A 177 MET cc_start: 0.7971 (pmt) cc_final: 0.7679 (pmt) REVERT: H 65 GLU cc_start: 0.7237 (pt0) cc_final: 0.6992 (pt0) REVERT: H 78 MET cc_start: 0.6678 (tpp) cc_final: 0.5915 (tpt) REVERT: H 100 MET cc_start: 0.7442 (OUTLIER) cc_final: 0.7159 (ttp) REVERT: H 109 ASP cc_start: 0.7218 (t0) cc_final: 0.7008 (t0) REVERT: H 134 MET cc_start: 0.8635 (mtm) cc_final: 0.8410 (mpp) REVERT: H 135 ASP cc_start: 0.8258 (m-30) cc_final: 0.8014 (m-30) REVERT: L 132 LYS cc_start: 0.7542 (mmmm) cc_final: 0.7180 (mmmm) outliers start: 14 outliers final: 4 residues processed: 72 average time/residue: 1.2160 time to fit residues: 90.5261 Evaluate side-chains 73 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 66 time to evaluate : 0.482 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS L 55 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 4117 Z= 0.306 Angle : 0.592 5.657 5594 Z= 0.312 Chirality : 0.046 0.203 634 Planarity : 0.004 0.041 706 Dihedral : 6.257 50.718 665 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.06 % Allowed : 16.02 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.44 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.88 (0.35), residues: 212 loop : -0.13 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 66 HIS 0.005 0.001 HIS A 245 PHE 0.024 0.002 PHE A 175 TYR 0.015 0.002 TYR A 28 ARG 0.003 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 68 time to evaluate : 0.437 Fit side-chains REVERT: A 80 ASP cc_start: 0.6366 (t0) cc_final: 0.6123 (t0) REVERT: A 169 GLU cc_start: 0.7971 (OUTLIER) cc_final: 0.7017 (tm-30) REVERT: A 173 GLN cc_start: 0.8447 (OUTLIER) cc_final: 0.7916 (mp10) REVERT: H 65 GLU cc_start: 0.7293 (pt0) cc_final: 0.7020 (pt0) REVERT: H 78 MET cc_start: 0.6692 (tpp) cc_final: 0.5938 (tpt) REVERT: H 100 MET cc_start: 0.7661 (OUTLIER) cc_final: 0.7240 (ttp) REVERT: H 134 MET cc_start: 0.8629 (mtm) cc_final: 0.8408 (mpp) REVERT: H 135 ASP cc_start: 0.8272 (m-30) cc_final: 0.8049 (m-30) outliers start: 9 outliers final: 5 residues processed: 71 average time/residue: 1.1216 time to fit residues: 82.5491 Evaluate side-chains 72 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 0.3980 chunk 46 optimal weight: 4.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 0.0010 chunk 24 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 5 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 137 ASN A 245 HIS H 58 GLN L 55 ASN L 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7958 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4117 Z= 0.222 Angle : 0.580 5.315 5594 Z= 0.311 Chirality : 0.045 0.192 634 Planarity : 0.004 0.039 706 Dihedral : 5.961 51.194 665 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.27 % Favored : 97.73 % Rotamer: Outliers : 2.52 % Allowed : 17.62 % Favored : 79.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.51 (0.39), residues: 485 helix: None (None), residues: 0 sheet: 0.93 (0.36), residues: 212 loop : -0.09 (0.38), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.006 0.001 HIS A 245 PHE 0.018 0.002 PHE A 175 TYR 0.013 0.001 TYR H 99 ARG 0.005 0.001 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 67 time to evaluate : 0.461 Fit side-chains REVERT: A 80 ASP cc_start: 0.6340 (t0) cc_final: 0.6095 (t0) REVERT: A 169 GLU cc_start: 0.7914 (OUTLIER) cc_final: 0.6994 (tm-30) REVERT: A 173 GLN cc_start: 0.8412 (OUTLIER) cc_final: 0.7873 (mp10) REVERT: H 53 MET cc_start: 0.7845 (tpp) cc_final: 0.7504 (tpt) REVERT: H 65 GLU cc_start: 0.7278 (pt0) cc_final: 0.6966 (pt0) REVERT: H 78 MET cc_start: 0.6674 (tpp) cc_final: 0.5919 (tpt) REVERT: H 100 MET cc_start: 0.7582 (OUTLIER) cc_final: 0.7207 (ttp) REVERT: H 135 ASP cc_start: 0.8257 (m-30) cc_final: 0.8019 (m-30) REVERT: L 24 MET cc_start: 0.7354 (mmt) cc_final: 0.6451 (mmt) outliers start: 11 outliers final: 5 residues processed: 72 average time/residue: 1.1194 time to fit residues: 83.6770 Evaluate side-chains 73 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 65 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 246 ARG Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 0.8980 chunk 39 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 46 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 9 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 overall best weight: 0.9782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS H 58 GLN L 55 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.2551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 4117 Z= 0.321 Angle : 0.610 5.587 5594 Z= 0.322 Chirality : 0.047 0.201 634 Planarity : 0.004 0.039 706 Dihedral : 5.946 50.466 665 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.97 % Allowed : 16.93 % Favored : 80.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.44 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.84 (0.35), residues: 220 loop : -0.13 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 66 HIS 0.007 0.001 HIS A 245 PHE 0.025 0.002 PHE A 175 TYR 0.015 0.002 TYR A 28 ARG 0.003 0.001 ARG A 273 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.456 Fit side-chains REVERT: A 80 ASP cc_start: 0.6269 (t0) cc_final: 0.6026 (t0) REVERT: A 131 CYS cc_start: 0.7185 (OUTLIER) cc_final: 0.6639 (m) REVERT: A 169 GLU cc_start: 0.7980 (OUTLIER) cc_final: 0.7021 (tm-30) REVERT: A 173 GLN cc_start: 0.8451 (OUTLIER) cc_final: 0.7923 (mp10) REVERT: A 177 MET cc_start: 0.7968 (pmt) cc_final: 0.7717 (pmt) REVERT: H 65 GLU cc_start: 0.7346 (pt0) cc_final: 0.7025 (pt0) REVERT: H 100 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7375 (ttp) REVERT: H 135 ASP cc_start: 0.8289 (m-30) cc_final: 0.8067 (m-30) outliers start: 13 outliers final: 6 residues processed: 74 average time/residue: 1.0914 time to fit residues: 83.5162 Evaluate side-chains 75 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 65 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 117 THR Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 36 optimal weight: 3.9990 chunk 42 optimal weight: 0.9990 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.8980 chunk 43 optimal weight: 0.0870 chunk 25 optimal weight: 2.9990 chunk 18 optimal weight: 0.0060 overall best weight: 0.4574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS A 245 HIS H 58 GLN L 55 ASN L 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4117 Z= 0.184 Angle : 0.559 5.835 5594 Z= 0.298 Chirality : 0.044 0.189 634 Planarity : 0.003 0.039 706 Dihedral : 5.643 51.685 665 Min Nonbonded Distance : 2.429 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.97 % Allowed : 18.08 % Favored : 78.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.41 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.83 (0.35), residues: 220 loop : -0.16 (0.39), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 66 HIS 0.006 0.001 HIS A 245 PHE 0.017 0.001 PHE H 70 TYR 0.010 0.001 TYR H 99 ARG 0.004 0.000 ARG A 190 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.519 Fit side-chains REVERT: A 80 ASP cc_start: 0.6205 (t0) cc_final: 0.5957 (t0) REVERT: A 131 CYS cc_start: 0.7042 (OUTLIER) cc_final: 0.6463 (m) REVERT: A 158 ARG cc_start: 0.8980 (mmt180) cc_final: 0.8764 (mmt180) REVERT: A 169 GLU cc_start: 0.7920 (OUTLIER) cc_final: 0.7023 (tm-30) REVERT: A 173 GLN cc_start: 0.8402 (OUTLIER) cc_final: 0.7846 (mp10) REVERT: A 177 MET cc_start: 0.7941 (pmt) cc_final: 0.7683 (pmt) REVERT: H 53 MET cc_start: 0.7750 (tpp) cc_final: 0.7376 (tpt) REVERT: H 65 GLU cc_start: 0.7315 (pt0) cc_final: 0.6961 (pt0) REVERT: H 100 MET cc_start: 0.7613 (OUTLIER) cc_final: 0.7201 (ttp) REVERT: H 135 ASP cc_start: 0.8276 (m-30) cc_final: 0.8039 (m-30) REVERT: L 24 MET cc_start: 0.7305 (mmt) cc_final: 0.6644 (mmt) REVERT: L 132 LYS cc_start: 0.7636 (mmmm) cc_final: 0.7412 (mmmm) outliers start: 13 outliers final: 5 residues processed: 74 average time/residue: 1.1048 time to fit residues: 85.0138 Evaluate side-chains 75 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 66 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 131 CYS Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 45 optimal weight: 0.8980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS H 58 GLN L 55 ASN L 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7990 moved from start: 0.2761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 4117 Z= 0.353 Angle : 0.636 7.204 5594 Z= 0.335 Chirality : 0.048 0.205 634 Planarity : 0.004 0.038 706 Dihedral : 5.934 50.251 665 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 7.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.97 % Allowed : 19.22 % Favored : 77.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.25 (0.38), residues: 485 helix: None (None), residues: 0 sheet: 0.84 (0.35), residues: 212 loop : -0.35 (0.37), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 66 HIS 0.008 0.001 HIS A 245 PHE 0.026 0.002 PHE A 175 TYR 0.016 0.002 TYR A 28 ARG 0.004 0.001 ARG A 158 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 67 time to evaluate : 0.454 Fit side-chains REVERT: A 80 ASP cc_start: 0.6240 (t0) cc_final: 0.6006 (t0) REVERT: A 158 ARG cc_start: 0.9095 (mmt180) cc_final: 0.8801 (mmt180) REVERT: A 169 GLU cc_start: 0.8011 (OUTLIER) cc_final: 0.7060 (tm-30) REVERT: A 173 GLN cc_start: 0.8440 (OUTLIER) cc_final: 0.7918 (mp10) REVERT: A 177 MET cc_start: 0.8024 (pmt) cc_final: 0.7764 (pmt) REVERT: H 65 GLU cc_start: 0.7346 (pt0) cc_final: 0.7020 (pt0) REVERT: H 67 MET cc_start: 0.8028 (mtm) cc_final: 0.7785 (ttm) REVERT: H 100 MET cc_start: 0.7808 (OUTLIER) cc_final: 0.7449 (ttp) REVERT: H 135 ASP cc_start: 0.8306 (m-30) cc_final: 0.8076 (m-30) REVERT: L 24 MET cc_start: 0.7200 (mmt) cc_final: 0.6501 (mmt) outliers start: 13 outliers final: 6 residues processed: 72 average time/residue: 1.0851 time to fit residues: 81.1044 Evaluate side-chains 74 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 65 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain L residue 47 GLN Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 1.9990 chunk 38 optimal weight: 1.9990 chunk 3 optimal weight: 0.9980 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 0.6980 chunk 30 optimal weight: 0.0870 chunk 40 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN A 69 HIS H 58 GLN L 55 ASN L 62 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7964 moved from start: 0.2777 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 4117 Z= 0.244 Angle : 0.593 5.868 5594 Z= 0.316 Chirality : 0.045 0.172 634 Planarity : 0.004 0.038 706 Dihedral : 5.957 51.247 665 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.29 % Allowed : 19.45 % Favored : 78.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.77 (0.35), residues: 212 loop : -0.42 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.010 0.001 HIS A 245 PHE 0.019 0.002 PHE A 175 TYR 0.013 0.002 TYR A 28 ARG 0.004 0.001 ARG A 158 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 970 Ramachandran restraints generated. 485 Oldfield, 0 Emsley, 485 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 66 time to evaluate : 0.389 Fit side-chains REVERT: A 80 ASP cc_start: 0.6222 (t0) cc_final: 0.6006 (t0) REVERT: A 169 GLU cc_start: 0.7935 (OUTLIER) cc_final: 0.7052 (tm-30) REVERT: A 173 GLN cc_start: 0.8421 (OUTLIER) cc_final: 0.7884 (mp10) REVERT: A 177 MET cc_start: 0.7996 (pmt) cc_final: 0.7745 (pmt) REVERT: H 53 MET cc_start: 0.7826 (tpp) cc_final: 0.7420 (tpt) REVERT: H 65 GLU cc_start: 0.7428 (pt0) cc_final: 0.7077 (pt0) REVERT: H 100 MET cc_start: 0.7714 (OUTLIER) cc_final: 0.7341 (ttp) REVERT: H 135 ASP cc_start: 0.8300 (m-30) cc_final: 0.8074 (m-30) REVERT: L 24 MET cc_start: 0.7051 (mmt) cc_final: 0.6636 (mmt) outliers start: 10 outliers final: 6 residues processed: 70 average time/residue: 1.1328 time to fit residues: 82.1752 Evaluate side-chains 73 residues out of total 437 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 64 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 124 THR Chi-restraints excluded: chain A residue 143 VAL Chi-restraints excluded: chain A residue 169 GLU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain H residue 24 VAL Chi-restraints excluded: chain H residue 30 VAL Chi-restraints excluded: chain H residue 100 MET Chi-restraints excluded: chain H residue 146 SER Chi-restraints excluded: chain L residue 122 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 0.8980 chunk 7 optimal weight: 0.5980 chunk 33 optimal weight: 3.9990 chunk 2 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 43 optimal weight: 0.0670 chunk 25 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 overall best weight: 0.8920 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 14 GLN H 58 GLN L 55 ASN L 62 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3887 r_free = 0.3887 target = 0.141383 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3331 r_free = 0.3331 target = 0.097916 restraints weight = 5579.706| |-----------------------------------------------------------------------------| r_work (start): 0.3288 rms_B_bonded: 2.21 r_work: 0.3189 rms_B_bonded: 2.38 restraints_weight: 0.5000 r_work: 0.3085 rms_B_bonded: 3.90 restraints_weight: 0.2500 r_work (final): 0.3085 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.2828 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.071 4117 Z= 0.303 Angle : 0.619 6.540 5594 Z= 0.329 Chirality : 0.046 0.174 634 Planarity : 0.004 0.039 706 Dihedral : 5.994 50.704 665 Min Nonbonded Distance : 2.397 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.09 % Favored : 96.91 % Rotamer: Outliers : 2.29 % Allowed : 19.68 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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 (0.37), residues: 485 helix: None (None), residues: 0 sheet: 0.75 (0.35), residues: 212 loop : -0.47 (0.36), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 66 HIS 0.002 0.001 HIS A 49 PHE 0.024 0.002 PHE A 175 TYR 0.014 0.002 TYR A 28 ARG 0.005 0.001 ARG A 158 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2307.90 seconds wall clock time: 43 minutes 21.87 seconds (2601.87 seconds total)