Starting phenix.real_space_refine on Mon Sep 23 22:19:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgi_37222/09_2024/8kgi_37222.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgi_37222/09_2024/8kgi_37222.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgi_37222/09_2024/8kgi_37222.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgi_37222/09_2024/8kgi_37222.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgi_37222/09_2024/8kgi_37222.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8kgi_37222/09_2024/8kgi_37222.cif" } resolution = 3.2 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= -0.002 sd= 0.048 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 32 5.16 5 C 3890 2.51 5 N 880 2.21 5 O 964 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5766 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2883 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 93 Chain: "B" Number of atoms: 2883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 391, 2883 Classifications: {'peptide': 391} Incomplete info: {'truncation_to_alanine': 40} Link IDs: {'PTRANS': 20, 'TRANS': 370} Chain breaks: 3 Unresolved non-hydrogen bonds: 150 Unresolved non-hydrogen angles: 187 Unresolved non-hydrogen dihedrals: 122 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 3, 'GLU:plan': 3, 'ARG:plan': 9} Unresolved non-hydrogen planarities: 93 Time building chain proxies: 4.12, per 1000 atoms: 0.71 Number of scatterers: 5766 At special positions: 0 Unit cell: (79.22, 103.452, 73.628, 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 32 16.00 O 964 8.00 N 880 7.00 C 3890 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.46 Conformation dependent library (CDL) restraints added in 693.5 milliseconds 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1452 Finding SS restraints... Secondary structure from input PDB file: 42 helices and 0 sheets defined 85.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.54 Creating SS restraints... Processing helix chain 'A' and resid 26 through 29 removed outlier: 3.713A pdb=" N GLY A 29 " --> pdb=" O SER A 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 26 through 29' Processing helix chain 'A' and resid 30 through 55 removed outlier: 4.310A pdb=" N PHE A 34 " --> pdb=" O ASN A 30 " (cutoff:3.500A) Processing helix chain 'A' and resid 55 through 63 Processing helix chain 'A' and resid 66 through 91 removed outlier: 4.419A pdb=" N SER A 70 " --> pdb=" O SER A 66 " (cutoff:3.500A) removed outlier: 4.532A pdb=" N GLY A 71 " --> pdb=" O SER A 67 " (cutoff:3.500A) removed outlier: 3.774A pdb=" N GLU A 78 " --> pdb=" O SER A 74 " (cutoff:3.500A) removed outlier: 4.119A pdb=" N ASN A 81 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 4.282A pdb=" N ILE A 86 " --> pdb=" O ALA A 82 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 87 " --> pdb=" O ILE A 83 " (cutoff:3.500A) removed outlier: 3.816A pdb=" N PHE A 91 " --> pdb=" O PHE A 87 " (cutoff:3.500A) Processing helix chain 'A' and resid 96 through 114 Processing helix chain 'A' and resid 116 through 121 Processing helix chain 'A' and resid 168 through 184 removed outlier: 3.647A pdb=" N LEU A 172 " --> pdb=" O SER A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 187 through 198 Processing helix chain 'A' and resid 203 through 217 removed outlier: 3.524A pdb=" N SER A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N PHE A 217 " --> pdb=" O ALA A 213 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 231 removed outlier: 4.176A pdb=" N GLN A 231 " --> pdb=" O SER A 227 " (cutoff:3.500A) Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 256 through 273 removed outlier: 3.876A pdb=" N GLY A 260 " --> pdb=" O ALA A 256 " (cutoff:3.500A) Processing helix chain 'A' and resid 274 through 278 Processing helix chain 'A' and resid 310 through 324 Proline residue: A 316 - end of helix Processing helix chain 'A' and resid 325 through 358 Processing helix chain 'A' and resid 363 through 390 Proline residue: A 374 - end of helix Processing helix chain 'A' and resid 396 through 412 Processing helix chain 'A' and resid 412 through 420 removed outlier: 3.541A pdb=" N MET A 418 " --> pdb=" O PRO A 414 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N GLY A 419 " --> pdb=" O LEU A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 515 through 544 removed outlier: 4.383A pdb=" N ASN A 534 " --> pdb=" O CYS A 530 " (cutoff:3.500A) Proline residue: A 535 - end of helix removed outlier: 3.818A pdb=" N VAL A 544 " --> pdb=" O VAL A 540 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 547 No H-bonds generated for 'chain 'A' and resid 545 through 547' Processing helix chain 'A' and resid 548 through 566 Processing helix chain 'B' and resid 26 through 29 removed outlier: 3.713A pdb=" N GLY B 29 " --> pdb=" O SER B 26 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 26 through 29' Processing helix chain 'B' and resid 30 through 55 removed outlier: 4.315A pdb=" N PHE B 34 " --> pdb=" O ASN B 30 " (cutoff:3.500A) Processing helix chain 'B' and resid 55 through 63 Processing helix chain 'B' and resid 66 through 91 removed outlier: 4.417A pdb=" N SER B 70 " --> pdb=" O SER B 66 " (cutoff:3.500A) removed outlier: 4.531A pdb=" N GLY B 71 " --> pdb=" O SER B 67 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLU B 78 " --> pdb=" O SER B 74 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N ASN B 81 " --> pdb=" O ASN B 77 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N ILE B 86 " --> pdb=" O ALA B 82 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N PHE B 87 " --> pdb=" O ILE B 83 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N PHE B 91 " --> pdb=" O PHE B 87 " (cutoff:3.500A) Processing helix chain 'B' and resid 96 through 114 Processing helix chain 'B' and resid 116 through 121 Processing helix chain 'B' and resid 168 through 184 removed outlier: 3.645A pdb=" N LEU B 172 " --> pdb=" O SER B 168 " (cutoff:3.500A) Processing helix chain 'B' and resid 187 through 198 Processing helix chain 'B' and resid 203 through 216 removed outlier: 3.502A pdb=" N SER B 215 " --> pdb=" O LEU B 211 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 231 removed outlier: 4.173A pdb=" N GLN B 231 " --> pdb=" O SER B 227 " (cutoff:3.500A) Processing helix chain 'B' and resid 242 through 247 Processing helix chain 'B' and resid 256 through 273 removed outlier: 3.876A pdb=" N GLY B 260 " --> pdb=" O ALA B 256 " (cutoff:3.500A) Processing helix chain 'B' and resid 274 through 278 Processing helix chain 'B' and resid 310 through 324 Proline residue: B 316 - end of helix Processing helix chain 'B' and resid 325 through 358 Processing helix chain 'B' and resid 363 through 390 Proline residue: B 374 - end of helix Processing helix chain 'B' and resid 396 through 412 Processing helix chain 'B' and resid 412 through 420 removed outlier: 3.540A pdb=" N MET B 418 " --> pdb=" O PRO B 414 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N GLY B 419 " --> pdb=" O LEU B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 515 through 544 removed outlier: 4.387A pdb=" N ASN B 534 " --> pdb=" O CYS B 530 " (cutoff:3.500A) Proline residue: B 535 - end of helix removed outlier: 3.817A pdb=" N VAL B 544 " --> pdb=" O VAL B 540 " (cutoff:3.500A) Processing helix chain 'B' and resid 545 through 547 No H-bonds generated for 'chain 'B' and resid 545 through 547' Processing helix chain 'B' and resid 548 through 566 450 hydrogen bonds defined for protein. 1338 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: 1.58 Time building geometry restraints manager: 1.69 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: 1672 1.34 - 1.46: 939 1.46 - 1.57: 3253 1.57 - 1.69: 0 1.69 - 1.81: 52 Bond restraints: 5916 Sorted by residual: bond pdb=" CB VAL A 540 " pdb=" CG2 VAL A 540 " ideal model delta sigma weight residual 1.521 1.484 0.037 3.30e-02 9.18e+02 1.23e+00 bond pdb=" CB VAL B 540 " pdb=" CG2 VAL B 540 " ideal model delta sigma weight residual 1.521 1.486 0.035 3.30e-02 9.18e+02 1.10e+00 bond pdb=" CG LEU B 211 " pdb=" CD1 LEU B 211 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.90e-01 bond pdb=" CG LEU A 211 " pdb=" CD1 LEU A 211 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.85e-01 bond pdb=" CB GLN B 335 " pdb=" CG GLN B 335 " ideal model delta sigma weight residual 1.520 1.492 0.028 3.00e-02 1.11e+03 8.69e-01 ... (remaining 5911 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 7638 1.21 - 2.42: 311 2.42 - 3.63: 70 3.63 - 4.83: 27 4.83 - 6.04: 24 Bond angle restraints: 8070 Sorted by residual: angle pdb=" C MET A 538 " pdb=" N MET A 539 " pdb=" CA MET A 539 " ideal model delta sigma weight residual 120.31 116.65 3.66 1.52e+00 4.33e-01 5.81e+00 angle pdb=" C MET B 538 " pdb=" N MET B 539 " pdb=" CA MET B 539 " ideal model delta sigma weight residual 120.31 116.67 3.64 1.52e+00 4.33e-01 5.72e+00 angle pdb=" C VAL A 239 " pdb=" N ASN A 240 " pdb=" CA ASN A 240 " ideal model delta sigma weight residual 121.54 125.74 -4.20 1.91e+00 2.74e-01 4.84e+00 angle pdb=" C VAL B 239 " pdb=" N ASN B 240 " pdb=" CA ASN B 240 " ideal model delta sigma weight residual 121.54 125.73 -4.19 1.91e+00 2.74e-01 4.81e+00 angle pdb=" N ASN B 534 " pdb=" CA ASN B 534 " pdb=" C ASN B 534 " ideal model delta sigma weight residual 109.81 114.57 -4.76 2.21e+00 2.05e-01 4.65e+00 ... (remaining 8065 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.67: 3061 15.67 - 31.35: 248 31.35 - 47.02: 72 47.02 - 62.70: 11 62.70 - 78.37: 10 Dihedral angle restraints: 3402 sinusoidal: 1154 harmonic: 2248 Sorted by residual: dihedral pdb=" CB MET A 418 " pdb=" CG MET A 418 " pdb=" SD MET A 418 " pdb=" CE MET A 418 " ideal model delta sinusoidal sigma weight residual -60.00 -113.12 53.12 3 1.50e+01 4.44e-03 9.18e+00 dihedral pdb=" CB MET B 418 " pdb=" CG MET B 418 " pdb=" SD MET B 418 " pdb=" CE MET B 418 " ideal model delta sinusoidal sigma weight residual -60.00 -113.04 53.04 3 1.50e+01 4.44e-03 9.17e+00 dihedral pdb=" CG LYS A 549 " pdb=" CD LYS A 549 " pdb=" CE LYS A 549 " pdb=" NZ LYS A 549 " ideal model delta sinusoidal sigma weight residual -180.00 -130.06 -49.94 3 1.50e+01 4.44e-03 8.84e+00 ... (remaining 3399 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 591 0.032 - 0.064: 239 0.064 - 0.095: 116 0.095 - 0.127: 32 0.127 - 0.159: 2 Chirality restraints: 980 Sorted by residual: chirality pdb=" CB THR A 403 " pdb=" CA THR A 403 " pdb=" OG1 THR A 403 " pdb=" CG2 THR A 403 " both_signs ideal model delta sigma weight residual False 2.55 2.39 0.16 2.00e-01 2.50e+01 6.30e-01 chirality pdb=" CB THR B 403 " pdb=" CA THR B 403 " pdb=" OG1 THR B 403 " pdb=" CG2 THR B 403 " both_signs ideal model delta sigma weight residual False 2.55 2.40 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CA SER A 568 " pdb=" N SER A 568 " pdb=" C SER A 568 " pdb=" CB SER A 568 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 977 not shown) Planarity restraints: 986 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE B 311 " 0.010 2.00e-02 2.50e+03 9.37e-03 1.54e+00 pdb=" CG PHE B 311 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE B 311 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE B 311 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE B 311 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE B 311 " 0.005 2.00e-02 2.50e+03 pdb=" CZ PHE B 311 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 311 " -0.010 2.00e-02 2.50e+03 9.09e-03 1.45e+00 pdb=" CG PHE A 311 " 0.021 2.00e-02 2.50e+03 pdb=" CD1 PHE A 311 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 311 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 311 " -0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 311 " -0.005 2.00e-02 2.50e+03 pdb=" CZ PHE A 311 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 413 " -0.019 5.00e-02 4.00e+02 2.88e-02 1.33e+00 pdb=" N PRO A 414 " 0.050 5.00e-02 4.00e+02 pdb=" CA PRO A 414 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 414 " -0.016 5.00e-02 4.00e+02 ... (remaining 983 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1755 2.82 - 3.34: 6423 3.34 - 3.86: 9649 3.86 - 4.38: 10123 4.38 - 4.90: 18141 Nonbonded interactions: 46091 Sorted by model distance: nonbonded pdb=" OH TYR B 194 " pdb=" O PRO B 279 " model vdw 2.303 3.040 nonbonded pdb=" OH TYR A 194 " pdb=" O PRO A 279 " model vdw 2.308 3.040 nonbonded pdb=" OG SER A 393 " pdb=" N LEU A 394 " model vdw 2.318 3.120 nonbonded pdb=" OG SER B 393 " pdb=" N LEU B 394 " model vdw 2.318 3.120 nonbonded pdb=" NH1 ARG A 97 " pdb=" OG SER A 193 " model vdw 2.342 3.120 ... (remaining 46086 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 2.050 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: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.960 Find NCS groups from input model: 0.310 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 : 0.003 0.037 5916 Z= 0.211 Angle : 0.668 6.042 8070 Z= 0.339 Chirality : 0.043 0.159 980 Planarity : 0.004 0.029 986 Dihedral : 13.818 78.370 1950 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 0.00 % Allowed : 0.51 % Favored : 99.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.76 (0.32), residues: 766 helix: 2.49 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -0.84 (0.53), residues: 162 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 257 HIS 0.001 0.000 HIS A 119 PHE 0.021 0.001 PHE B 311 TYR 0.015 0.002 TYR B 90 ARG 0.002 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.636 Fit side-chains REVERT: B 125 TYR cc_start: 0.6453 (t80) cc_final: 0.6029 (t80) outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.1625 time to fit residues: 32.6730 Evaluate side-chains 129 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 7.9990 chunk 59 optimal weight: 0.6980 chunk 32 optimal weight: 3.9990 chunk 20 optimal weight: 0.8980 chunk 39 optimal weight: 8.9990 chunk 31 optimal weight: 0.6980 chunk 61 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.5980 chunk 45 optimal weight: 0.8980 chunk 70 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 77 ASN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7253 moved from start: 0.1074 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5916 Z= 0.239 Angle : 0.647 7.417 8070 Z= 0.313 Chirality : 0.044 0.312 980 Planarity : 0.004 0.031 986 Dihedral : 3.773 14.291 806 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % Rotamer: Outliers : 1.54 % Allowed : 11.30 % Favored : 87.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.07 (0.32), residues: 766 helix: 2.64 (0.21), residues: 606 sheet: None (None), residues: 0 loop : -0.44 (0.57), residues: 160 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 257 HIS 0.001 0.001 HIS B 533 PHE 0.023 0.001 PHE B 348 TYR 0.014 0.001 TYR A 537 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 136 time to evaluate : 0.555 Fit side-chains REVERT: A 60 GLU cc_start: 0.8499 (tm-30) cc_final: 0.7906 (tm-30) REVERT: A 519 ILE cc_start: 0.9100 (OUTLIER) cc_final: 0.8861 (mm) REVERT: B 60 GLU cc_start: 0.8492 (tm-30) cc_final: 0.7900 (tm-30) REVERT: B 519 ILE cc_start: 0.9101 (OUTLIER) cc_final: 0.8880 (mm) outliers start: 9 outliers final: 2 residues processed: 142 average time/residue: 0.1606 time to fit residues: 30.1376 Evaluate side-chains 133 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 129 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 327 LEU Chi-restraints excluded: chain A residue 519 ILE Chi-restraints excluded: chain B residue 327 LEU Chi-restraints excluded: chain B residue 519 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 7.9990 chunk 21 optimal weight: 0.2980 chunk 58 optimal weight: 0.8980 chunk 48 optimal weight: 0.1980 chunk 19 optimal weight: 0.6980 chunk 70 optimal weight: 0.0570 chunk 76 optimal weight: 0.5980 chunk 63 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 56 optimal weight: 9.9990 chunk 53 optimal weight: 0.7980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7230 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5916 Z= 0.182 Angle : 0.615 7.583 8070 Z= 0.297 Chirality : 0.045 0.316 980 Planarity : 0.004 0.030 986 Dihedral : 3.730 13.023 806 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.23 % Allowed : 15.07 % Favored : 82.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.31), residues: 766 helix: 2.69 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.39 (0.57), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 257 HIS 0.001 0.000 HIS B 533 PHE 0.022 0.001 PHE B 348 TYR 0.016 0.001 TYR A 90 ARG 0.001 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 152 time to evaluate : 0.593 Fit side-chains REVERT: A 60 GLU cc_start: 0.8420 (tm-30) cc_final: 0.7787 (tm-30) REVERT: B 60 GLU cc_start: 0.8411 (tm-30) cc_final: 0.7781 (tm-30) REVERT: B 200 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.7847 (pm20) outliers start: 13 outliers final: 8 residues processed: 154 average time/residue: 0.1555 time to fit residues: 31.7456 Evaluate side-chains 141 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 132 time to evaluate : 0.612 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.9990 chunk 7 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 9.9990 chunk 75 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 62 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 372 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7277 moved from start: 0.1549 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5916 Z= 0.245 Angle : 0.641 7.776 8070 Z= 0.312 Chirality : 0.044 0.290 980 Planarity : 0.004 0.030 986 Dihedral : 3.821 14.605 806 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 9.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.52 % Favored : 96.48 % Rotamer: Outliers : 2.74 % Allowed : 18.66 % Favored : 78.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.19 (0.32), residues: 766 helix: 2.73 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.48 (0.57), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 257 HIS 0.001 0.000 HIS B 533 PHE 0.020 0.001 PHE B 348 TYR 0.017 0.001 TYR A 90 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 145 time to evaluate : 0.617 Fit side-chains REVERT: A 60 GLU cc_start: 0.8412 (tm-30) cc_final: 0.7914 (tm-30) REVERT: A 378 LEU cc_start: 0.8585 (OUTLIER) cc_final: 0.8311 (tt) REVERT: A 537 TYR cc_start: 0.8196 (t80) cc_final: 0.7991 (t80) REVERT: B 60 GLU cc_start: 0.8406 (tm-30) cc_final: 0.7912 (tm-30) REVERT: B 200 GLU cc_start: 0.8334 (OUTLIER) cc_final: 0.7828 (pm20) REVERT: B 378 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8297 (tt) REVERT: B 537 TYR cc_start: 0.8161 (t80) cc_final: 0.7855 (t80) outliers start: 16 outliers final: 8 residues processed: 152 average time/residue: 0.1587 time to fit residues: 32.1197 Evaluate side-chains 151 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 140 time to evaluate : 0.602 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.6980 chunk 56 optimal weight: 4.9990 chunk 31 optimal weight: 1.9990 chunk 64 optimal weight: 4.9990 chunk 52 optimal weight: 2.9990 chunk 0 optimal weight: 5.9990 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 0.0050 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 overall best weight: 0.8996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 77 ASN ** B 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 moved from start: 0.1731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 5916 Z= 0.252 Angle : 0.652 7.516 8070 Z= 0.315 Chirality : 0.044 0.267 980 Planarity : 0.004 0.030 986 Dihedral : 3.882 19.715 806 Min Nonbonded Distance : 2.439 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.57 % Allowed : 21.23 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.32), residues: 766 helix: 2.70 (0.21), residues: 608 sheet: None (None), residues: 0 loop : -0.52 (0.57), residues: 158 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 257 HIS 0.001 0.000 HIS B 533 PHE 0.021 0.001 PHE B 366 TYR 0.012 0.001 TYR B 90 ARG 0.003 0.000 ARG B 389 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 148 time to evaluate : 0.524 Fit side-chains REVERT: A 60 GLU cc_start: 0.8402 (tm-30) cc_final: 0.7896 (tm-30) REVERT: A 378 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8310 (tt) REVERT: A 537 TYR cc_start: 0.8215 (t80) cc_final: 0.7993 (t80) REVERT: B 60 GLU cc_start: 0.8392 (tm-30) cc_final: 0.7892 (tm-30) REVERT: B 200 GLU cc_start: 0.8314 (OUTLIER) cc_final: 0.7799 (pm20) REVERT: B 378 LEU cc_start: 0.8608 (OUTLIER) cc_final: 0.8319 (tt) REVERT: B 537 TYR cc_start: 0.8220 (t80) cc_final: 0.7986 (t80) outliers start: 15 outliers final: 8 residues processed: 155 average time/residue: 0.1532 time to fit residues: 31.6718 Evaluate side-chains 149 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 95 VAL Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 95 VAL Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 75 optimal weight: 0.0870 chunk 62 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 39 optimal weight: 8.9990 chunk 72 optimal weight: 6.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 3.9990 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** A 350 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 ASN B 350 ASN B 372 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.1998 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 5916 Z= 0.235 Angle : 0.652 6.771 8070 Z= 0.316 Chirality : 0.045 0.272 980 Planarity : 0.004 0.031 986 Dihedral : 3.838 17.032 806 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.08 % Allowed : 21.58 % Favored : 75.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.14 (0.32), residues: 766 helix: 2.70 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.55 (0.58), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 257 HIS 0.001 0.000 HIS B 533 PHE 0.018 0.001 PHE B 348 TYR 0.012 0.001 TYR B 90 ARG 0.002 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 150 time to evaluate : 0.592 Fit side-chains REVERT: A 60 GLU cc_start: 0.8387 (tm-30) cc_final: 0.7737 (tm-30) REVERT: A 378 LEU cc_start: 0.8587 (OUTLIER) cc_final: 0.8315 (tt) REVERT: B 60 GLU cc_start: 0.8381 (tm-30) cc_final: 0.7738 (tm-30) REVERT: B 200 GLU cc_start: 0.8309 (OUTLIER) cc_final: 0.7788 (pm20) REVERT: B 378 LEU cc_start: 0.8596 (OUTLIER) cc_final: 0.8314 (tt) outliers start: 18 outliers final: 7 residues processed: 159 average time/residue: 0.1499 time to fit residues: 31.7820 Evaluate side-chains 153 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 143 time to evaluate : 0.552 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 0.5980 chunk 42 optimal weight: 4.9990 chunk 63 optimal weight: 0.7980 chunk 75 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.2980 chunk 34 optimal weight: 0.4980 chunk 46 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN A 350 ASN A 372 ASN B 372 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7280 moved from start: 0.2022 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.060 5916 Z= 0.208 Angle : 0.658 6.917 8070 Z= 0.318 Chirality : 0.044 0.241 980 Planarity : 0.004 0.031 986 Dihedral : 3.781 16.406 806 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 11.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.91 % Allowed : 23.12 % Favored : 73.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.13 (0.32), residues: 766 helix: 2.69 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.53 (0.57), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 257 HIS 0.001 0.000 HIS A 533 PHE 0.021 0.001 PHE A 366 TYR 0.009 0.001 TYR B 90 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 140 time to evaluate : 0.563 Fit side-chains REVERT: A 60 GLU cc_start: 0.8362 (tm-30) cc_final: 0.7715 (tm-30) REVERT: A 378 LEU cc_start: 0.8567 (OUTLIER) cc_final: 0.8300 (tt) REVERT: A 536 LEU cc_start: 0.7435 (OUTLIER) cc_final: 0.7194 (mt) REVERT: B 60 GLU cc_start: 0.8350 (tm-30) cc_final: 0.7708 (tm-30) REVERT: B 200 GLU cc_start: 0.8285 (OUTLIER) cc_final: 0.7753 (pm20) REVERT: B 378 LEU cc_start: 0.8564 (OUTLIER) cc_final: 0.8290 (tt) outliers start: 17 outliers final: 10 residues processed: 150 average time/residue: 0.1584 time to fit residues: 31.8606 Evaluate side-chains 155 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 141 time to evaluate : 0.601 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Chi-restraints excluded: chain B residue 540 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 0.7980 chunk 47 optimal weight: 2.9990 chunk 51 optimal weight: 0.6980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 2.9990 chunk 59 optimal weight: 0.9980 chunk 68 optimal weight: 0.5980 chunk 72 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7296 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 5916 Z= 0.238 Angle : 0.679 7.462 8070 Z= 0.330 Chirality : 0.044 0.194 980 Planarity : 0.004 0.030 986 Dihedral : 3.848 16.903 806 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.39 % Favored : 96.61 % Rotamer: Outliers : 2.91 % Allowed : 23.97 % Favored : 73.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.09 (0.32), residues: 766 helix: 2.64 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.43 (0.57), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 257 HIS 0.001 0.000 HIS B 533 PHE 0.020 0.001 PHE B 198 TYR 0.014 0.001 TYR B 194 ARG 0.003 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 145 time to evaluate : 0.485 Fit side-chains REVERT: A 60 GLU cc_start: 0.8373 (tm-30) cc_final: 0.7730 (tp30) REVERT: A 378 LEU cc_start: 0.8591 (OUTLIER) cc_final: 0.8316 (tt) REVERT: A 536 LEU cc_start: 0.7443 (OUTLIER) cc_final: 0.7203 (mt) REVERT: B 60 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7747 (tp30) REVERT: B 200 GLU cc_start: 0.8282 (OUTLIER) cc_final: 0.7743 (pm20) REVERT: B 378 LEU cc_start: 0.8586 (OUTLIER) cc_final: 0.8304 (tt) outliers start: 17 outliers final: 9 residues processed: 155 average time/residue: 0.1583 time to fit residues: 32.6772 Evaluate side-chains 157 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 144 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain A residue 540 VAL Chi-restraints excluded: chain B residue 86 ILE Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 1.9990 chunk 55 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 0.7980 chunk 69 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 74 optimal weight: 0.6980 chunk 45 optimal weight: 0.3980 chunk 35 optimal weight: 0.9990 chunk 51 optimal weight: 0.0870 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.7282 moved from start: 0.2172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.078 5916 Z= 0.220 Angle : 0.685 8.288 8070 Z= 0.332 Chirality : 0.045 0.228 980 Planarity : 0.004 0.031 986 Dihedral : 3.844 17.335 806 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer: Outliers : 2.57 % Allowed : 24.66 % Favored : 72.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.08 (0.32), residues: 766 helix: 2.59 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -0.30 (0.58), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 257 HIS 0.001 0.000 HIS B 533 PHE 0.021 0.001 PHE A 366 TYR 0.008 0.001 TYR A 90 ARG 0.004 0.000 ARG A 389 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 140 time to evaluate : 0.622 Fit side-chains REVERT: A 60 GLU cc_start: 0.8363 (tm-30) cc_final: 0.7762 (tp30) REVERT: A 378 LEU cc_start: 0.8580 (OUTLIER) cc_final: 0.8322 (tt) REVERT: A 536 LEU cc_start: 0.7378 (OUTLIER) cc_final: 0.7133 (mt) REVERT: B 60 GLU cc_start: 0.8360 (tm-30) cc_final: 0.7764 (tp30) REVERT: B 177 GLN cc_start: 0.8172 (tp40) cc_final: 0.7965 (tp40) REVERT: B 200 GLU cc_start: 0.8258 (OUTLIER) cc_final: 0.7719 (pm20) REVERT: B 378 LEU cc_start: 0.8572 (OUTLIER) cc_final: 0.8303 (tt) outliers start: 15 outliers final: 7 residues processed: 150 average time/residue: 0.1539 time to fit residues: 30.7049 Evaluate side-chains 149 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 138 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 6.9990 chunk 71 optimal weight: 0.0570 chunk 61 optimal weight: 0.0020 chunk 6 optimal weight: 0.0970 chunk 47 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 49 optimal weight: 6.9990 chunk 65 optimal weight: 8.9990 chunk 18 optimal weight: 0.2980 chunk 57 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 overall best weight: 0.6906 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7288 moved from start: 0.2345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 5916 Z= 0.238 Angle : 0.705 10.304 8070 Z= 0.341 Chirality : 0.045 0.246 980 Planarity : 0.004 0.031 986 Dihedral : 3.869 17.763 806 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 2.23 % Allowed : 25.17 % Favored : 72.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.98 (0.32), residues: 766 helix: 2.53 (0.21), residues: 612 sheet: None (None), residues: 0 loop : -0.38 (0.57), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 257 HIS 0.001 0.000 HIS A 533 PHE 0.021 0.001 PHE A 233 TYR 0.007 0.001 TYR B 90 ARG 0.004 0.000 ARG A 389 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1532 Ramachandran restraints generated. 766 Oldfield, 0 Emsley, 766 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 138 time to evaluate : 0.638 Fit side-chains REVERT: A 60 GLU cc_start: 0.8376 (tm-30) cc_final: 0.7772 (tp30) REVERT: A 378 LEU cc_start: 0.8597 (OUTLIER) cc_final: 0.8335 (tt) REVERT: A 536 LEU cc_start: 0.7402 (OUTLIER) cc_final: 0.7159 (mt) REVERT: B 60 GLU cc_start: 0.8367 (tm-30) cc_final: 0.7783 (tp30) REVERT: B 200 GLU cc_start: 0.8261 (OUTLIER) cc_final: 0.7717 (pm20) REVERT: B 378 LEU cc_start: 0.8581 (OUTLIER) cc_final: 0.8305 (tt) outliers start: 13 outliers final: 8 residues processed: 144 average time/residue: 0.1552 time to fit residues: 29.5349 Evaluate side-chains 149 residues out of total 664 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 137 time to evaluate : 0.581 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 ILE Chi-restraints excluded: chain A residue 179 LEU Chi-restraints excluded: chain A residue 215 SER Chi-restraints excluded: chain A residue 359 THR Chi-restraints excluded: chain A residue 371 VAL Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 536 LEU Chi-restraints excluded: chain B residue 200 GLU Chi-restraints excluded: chain B residue 215 SER Chi-restraints excluded: chain B residue 359 THR Chi-restraints excluded: chain B residue 371 VAL Chi-restraints excluded: chain B residue 378 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 70 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 GLN ** B 177 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.186065 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3688 r_free = 0.3688 target = 0.134277 restraints weight = 8491.977| |-----------------------------------------------------------------------------| r_work (start): 0.3701 rms_B_bonded: 3.29 r_work: 0.3527 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3527 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.074 5916 Z= 0.268 Angle : 0.716 10.014 8070 Z= 0.348 Chirality : 0.045 0.200 980 Planarity : 0.004 0.034 986 Dihedral : 3.882 17.840 806 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 1.88 % Allowed : 25.68 % Favored : 72.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.32), residues: 766 helix: 2.52 (0.21), residues: 610 sheet: None (None), residues: 0 loop : -0.45 (0.58), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 257 HIS 0.001 0.001 HIS B 533 PHE 0.020 0.001 PHE A 233 TYR 0.013 0.001 TYR B 194 ARG 0.004 0.000 ARG A 389 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1547.43 seconds wall clock time: 28 minutes 7.02 seconds (1687.02 seconds total)