Starting phenix.real_space_refine on Wed Mar 5 19:04:52 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7wef_32449/03_2025/7wef_32449.cif Found real_map, /net/cci-nas-00/data/ceres_data/7wef_32449/03_2025/7wef_32449.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7wef_32449/03_2025/7wef_32449.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7wef_32449/03_2025/7wef_32449.map" model { file = "/net/cci-nas-00/data/ceres_data/7wef_32449/03_2025/7wef_32449.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7wef_32449/03_2025/7wef_32449.cif" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2119 2.51 5 N 565 2.21 5 O 629 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 3328 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 902 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 5, 'TRANS': 114} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 2, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 17 Chain: "E" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 201, 1610 Classifications: {'peptide': 201} Link IDs: {'PTRANS': 12, 'TRANS': 188} Chain: "L" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 816 Classifications: {'peptide': 111} Link IDs: {'PTRANS': 8, 'TRANS': 102} Time building chain proxies: 3.71, per 1000 atoms: 1.11 Number of scatterers: 3328 At special positions: 0 Unit cell: (79.18, 85.6, 86.67, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 629 8.00 N 565 7.00 C 2119 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 95 " distance=2.03 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.04 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.04 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.73 Conformation dependent library (CDL) restraints added in 384.8 milliseconds 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 782 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 7.2% alpha, 28.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.40 Creating SS restraints... Processing helix chain 'C' and resid 28 through 32 removed outlier: 3.672A pdb=" N HIS C 32 " --> pdb=" O PHE C 29 " (cutoff:3.500A) Processing helix chain 'C' and resid 86 through 90 removed outlier: 3.993A pdb=" N THR C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing helix chain 'E' and resid 337 through 343 Processing helix chain 'E' and resid 366 through 371 removed outlier: 3.776A pdb=" N ASN E 370 " --> pdb=" O SER E 366 " (cutoff:3.500A) Processing helix chain 'E' and resid 404 through 411 removed outlier: 3.940A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA E 411 " --> pdb=" O ARG E 408 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 5 removed outlier: 4.209A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.985A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N TYR C 79 " --> pdb=" O THR C 70 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 57 through 59 removed outlier: 6.346A pdb=" N TRP C 36 " --> pdb=" O MET C 48 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ILE C 50 " --> pdb=" O ILE C 34 " (cutoff:3.500A) removed outlier: 6.336A pdb=" N ILE C 34 " --> pdb=" O ILE C 50 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.993A pdb=" N ASN E 354 " --> pdb=" O SER E 399 " (cutoff:3.500A) removed outlier: 3.618A pdb=" N SER E 399 " --> pdb=" O ASN E 354 " (cutoff:3.500A) removed outlier: 3.819A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA5, first strand: chain 'E' and resid 473 through 474 removed outlier: 3.584A pdb=" N TYR E 473 " --> pdb=" O TYR E 489 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N TYR E 489 " --> pdb=" O TYR E 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'L' and resid 9 through 12 removed outlier: 6.041A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.311A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 9 through 12 removed outlier: 3.528A pdb=" N ALA L 91 " --> pdb=" O VAL L 102 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N VAL L 102 " --> pdb=" O ALA L 91 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.557A pdb=" N VAL L 18 " --> pdb=" O ILE L 76 " (cutoff:3.500A) 87 hydrogen bonds defined for protein. 213 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: 0.88 Time building geometry restraints manager: 0.89 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1066 1.35 - 1.47: 943 1.47 - 1.59: 1395 1.59 - 1.71: 0 1.71 - 1.84: 18 Bond restraints: 3422 Sorted by residual: bond pdb=" N LEU C 104 " pdb=" CA LEU C 104 " ideal model delta sigma weight residual 1.465 1.452 0.013 1.31e-02 5.83e+03 9.85e-01 bond pdb=" CB CYS E 379 " pdb=" SG CYS E 379 " ideal model delta sigma weight residual 1.808 1.837 -0.029 3.30e-02 9.18e+02 7.49e-01 bond pdb=" CA THR E 333 " pdb=" CB THR E 333 " ideal model delta sigma weight residual 1.530 1.544 -0.014 1.69e-02 3.50e+03 6.96e-01 bond pdb=" CA ILE L 76 " pdb=" CB ILE L 76 " ideal model delta sigma weight residual 1.540 1.529 0.011 1.36e-02 5.41e+03 6.45e-01 bond pdb=" CB TRP C 47 " pdb=" CG TRP C 47 " ideal model delta sigma weight residual 1.498 1.475 0.023 3.10e-02 1.04e+03 5.72e-01 ... (remaining 3417 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.04: 4315 1.04 - 2.07: 254 2.07 - 3.11: 60 3.11 - 4.14: 29 4.14 - 5.18: 4 Bond angle restraints: 4662 Sorted by residual: angle pdb=" C ARG C 64 " pdb=" N ASP C 65 " pdb=" CA ASP C 65 " ideal model delta sigma weight residual 121.54 126.02 -4.48 1.91e+00 2.74e-01 5.51e+00 angle pdb=" C ILE E 332 " pdb=" N THR E 333 " pdb=" CA THR E 333 " ideal model delta sigma weight residual 121.54 125.79 -4.25 1.91e+00 2.74e-01 4.95e+00 angle pdb=" CA PHE C 107 " pdb=" C PHE C 107 " pdb=" N ASP C 108 " ideal model delta sigma weight residual 115.29 117.80 -2.51 1.18e+00 7.18e-01 4.54e+00 angle pdb=" C MET C 69 " pdb=" CA MET C 69 " pdb=" CB MET C 69 " ideal model delta sigma weight residual 110.24 113.20 -2.96 1.46e+00 4.69e-01 4.10e+00 angle pdb=" CA PHE C 107 " pdb=" C PHE C 107 " pdb=" O PHE C 107 " ideal model delta sigma weight residual 122.36 119.97 2.39 1.21e+00 6.83e-01 3.91e+00 ... (remaining 4657 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.33: 1805 16.33 - 32.66: 148 32.66 - 48.99: 38 48.99 - 65.32: 4 65.32 - 81.65: 5 Dihedral angle restraints: 2000 sinusoidal: 763 harmonic: 1237 Sorted by residual: dihedral pdb=" CB CYS E 480 " pdb=" SG CYS E 480 " pdb=" SG CYS E 488 " pdb=" CB CYS E 488 " ideal model delta sinusoidal sigma weight residual 93.00 159.95 -66.95 1 1.00e+01 1.00e-02 5.84e+01 dihedral pdb=" CA ILE C 51 " pdb=" C ILE C 51 " pdb=" N ASN C 52 " pdb=" CA ASN C 52 " ideal model delta harmonic sigma weight residual 180.00 162.64 17.36 0 5.00e+00 4.00e-02 1.21e+01 dihedral pdb=" CA ASP E 428 " pdb=" C ASP E 428 " pdb=" N PHE E 429 " pdb=" CA PHE E 429 " ideal model delta harmonic sigma weight residual -180.00 -163.76 -16.24 0 5.00e+00 4.00e-02 1.05e+01 ... (remaining 1997 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 278 0.030 - 0.060: 143 0.060 - 0.090: 51 0.090 - 0.120: 19 0.120 - 0.150: 5 Chirality restraints: 496 Sorted by residual: chirality pdb=" CA ILE C 51 " pdb=" N ILE C 51 " pdb=" C ILE C 51 " pdb=" CB ILE C 51 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.61e-01 chirality pdb=" CA ILE L 20 " pdb=" N ILE L 20 " pdb=" C ILE L 20 " pdb=" CB ILE L 20 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CA ILE E 434 " pdb=" N ILE E 434 " pdb=" C ILE E 434 " pdb=" CB ILE E 434 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.10e-01 ... (remaining 493 not shown) Planarity restraints: 604 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP C 47 " 0.012 2.00e-02 2.50e+03 1.66e-02 6.86e+00 pdb=" CG TRP C 47 " -0.042 2.00e-02 2.50e+03 pdb=" CD1 TRP C 47 " 0.028 2.00e-02 2.50e+03 pdb=" CD2 TRP C 47 " 0.003 2.00e-02 2.50e+03 pdb=" NE1 TRP C 47 " -0.009 2.00e-02 2.50e+03 pdb=" CE2 TRP C 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP C 47 " 0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 47 " -0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 47 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP C 47 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ASP C 72 " -0.025 5.00e-02 4.00e+02 3.73e-02 2.22e+00 pdb=" N PRO C 73 " 0.064 5.00e-02 4.00e+02 pdb=" CA PRO C 73 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO C 73 " -0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP C 108 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO C 109 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO C 109 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO C 109 " 0.019 5.00e-02 4.00e+02 ... (remaining 601 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 592 2.77 - 3.30: 2922 3.30 - 3.84: 4973 3.84 - 4.37: 5725 4.37 - 4.90: 10342 Nonbonded interactions: 24554 Sorted by model distance: nonbonded pdb=" ND2 ASN E 439 " pdb=" OE1 GLN E 506 " model vdw 2.239 3.120 nonbonded pdb=" OG1 THR C 28 " pdb=" OG SER C 31 " model vdw 2.300 3.040 nonbonded pdb=" O THR C 28 " pdb=" OG SER C 31 " model vdw 2.309 3.040 nonbonded pdb=" O ASN L 53 " pdb=" NH1 ARG L 55 " model vdw 2.313 3.120 nonbonded pdb=" OH TYR E 369 " pdb=" O PRO E 384 " model vdw 2.326 3.040 ... (remaining 24549 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 group one per residue 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: 3.390 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 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 0.029 3422 Z= 0.220 Angle : 0.624 5.176 4662 Z= 0.334 Chirality : 0.043 0.150 496 Planarity : 0.004 0.037 604 Dihedral : 12.721 81.647 1200 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 8.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.51 % Favored : 92.49 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.41), residues: 426 helix: -3.97 (0.48), residues: 26 sheet: 0.64 (0.49), residues: 135 loop : -1.38 (0.37), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.003 TRP C 47 HIS 0.002 0.001 HIS E 505 PHE 0.012 0.002 PHE E 374 TYR 0.015 0.001 TYR E 453 ARG 0.004 0.001 ARG E 509 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.334 Fit side-chains REVERT: C 106 TRP cc_start: 0.8053 (p-90) cc_final: 0.7845 (p-90) REVERT: E 346 ARG cc_start: 0.7386 (ttp80) cc_final: 0.6968 (ptm-80) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1511 time to fit residues: 11.2925 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 17 optimal weight: 0.0970 chunk 33 optimal weight: 0.0370 chunk 13 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 25 optimal weight: 0.0970 chunk 39 optimal weight: 3.9990 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.141948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3498 r_free = 0.3498 target = 0.118026 restraints weight = 4578.248| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3535 r_free = 0.3535 target = 0.121221 restraints weight = 2904.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3565 r_free = 0.3565 target = 0.123675 restraints weight = 2096.834| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.0920 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3422 Z= 0.180 Angle : 0.568 5.327 4662 Z= 0.295 Chirality : 0.042 0.160 496 Planarity : 0.004 0.037 604 Dihedral : 4.504 16.939 474 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.10 % Favored : 93.90 % Rotamer: Outliers : 1.12 % Allowed : 8.38 % Favored : 90.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.05 (0.41), residues: 426 helix: -3.82 (0.51), residues: 27 sheet: 0.89 (0.49), residues: 133 loop : -1.26 (0.37), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 103 HIS 0.001 0.001 HIS E 505 PHE 0.009 0.001 PHE C 63 TYR 0.008 0.001 TYR L 50 ARG 0.003 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 61 time to evaluate : 0.342 Fit side-chains REVERT: E 346 ARG cc_start: 0.7459 (ttp80) cc_final: 0.7150 (ptm-80) REVERT: E 406 GLU cc_start: 0.8111 (mt-10) cc_final: 0.7785 (tt0) outliers start: 4 outliers final: 3 residues processed: 63 average time/residue: 0.1565 time to fit residues: 12.1077 Evaluate side-chains 56 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 107 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 1.9990 chunk 40 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 6 optimal weight: 0.1980 chunk 18 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.9990 chunk 27 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 1.0186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.136885 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3433 r_free = 0.3433 target = 0.113449 restraints weight = 4640.891| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116286 restraints weight = 3060.147| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3496 r_free = 0.3496 target = 0.118432 restraints weight = 2264.958| |-----------------------------------------------------------------------------| r_work (final): 0.3496 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7484 moved from start: 0.1171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3422 Z= 0.297 Angle : 0.625 5.330 4662 Z= 0.324 Chirality : 0.044 0.155 496 Planarity : 0.004 0.035 604 Dihedral : 4.777 17.992 474 Min Nonbonded Distance : 2.592 Molprobity Statistics. All-atom Clashscore : 6.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 1.96 % Allowed : 10.89 % Favored : 87.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.21 (0.40), residues: 426 helix: -3.24 (0.72), residues: 21 sheet: 0.75 (0.48), residues: 133 loop : -1.50 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.003 TRP L 101 HIS 0.004 0.001 HIS E 505 PHE 0.017 0.002 PHE E 429 TYR 0.010 0.002 TYR E 453 ARG 0.002 0.000 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.380 Fit side-chains REVERT: E 346 ARG cc_start: 0.7455 (ttp80) cc_final: 0.7185 (ptm-80) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.1500 time to fit residues: 10.8303 Evaluate side-chains 57 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 7 optimal weight: 2.9990 chunk 17 optimal weight: 0.7980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 34 optimal weight: 7.9990 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 42 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3905 r_free = 0.3905 target = 0.149466 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.128328 restraints weight = 4720.061| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3673 r_free = 0.3673 target = 0.130987 restraints weight = 3262.355| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.132679 restraints weight = 2491.745| |-----------------------------------------------------------------------------| r_work (final): 0.3710 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3422 Z= 0.241 Angle : 0.585 5.208 4662 Z= 0.303 Chirality : 0.043 0.158 496 Planarity : 0.004 0.033 604 Dihedral : 4.696 21.157 474 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % Rotamer: Outliers : 2.79 % Allowed : 13.13 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.40), residues: 426 helix: -3.19 (0.72), residues: 21 sheet: 0.71 (0.48), residues: 133 loop : -1.57 (0.36), residues: 272 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 106 HIS 0.003 0.001 HIS E 505 PHE 0.012 0.002 PHE E 429 TYR 0.010 0.001 TYR E 423 ARG 0.002 0.000 ARG E 498 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.386 Fit side-chains REVERT: E 346 ARG cc_start: 0.7412 (ttp80) cc_final: 0.7185 (ptm-80) outliers start: 10 outliers final: 9 residues processed: 63 average time/residue: 0.1284 time to fit residues: 10.2706 Evaluate side-chains 63 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 54 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 22 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.0270 chunk 37 optimal weight: 0.9980 chunk 41 optimal weight: 2.9990 chunk 26 optimal weight: 0.0060 chunk 29 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 overall best weight: 0.4054 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.138927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115446 restraints weight = 4659.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3485 r_free = 0.3485 target = 0.118406 restraints weight = 3057.014| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3517 r_free = 0.3517 target = 0.120775 restraints weight = 2253.578| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 3422 Z= 0.195 Angle : 0.561 5.363 4662 Z= 0.290 Chirality : 0.042 0.160 496 Planarity : 0.004 0.033 604 Dihedral : 4.470 21.657 474 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.81 % Favored : 93.19 % Rotamer: Outliers : 2.79 % Allowed : 13.41 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.31 (0.40), residues: 426 helix: -3.13 (0.78), residues: 21 sheet: 0.44 (0.47), residues: 141 loop : -1.49 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.011 0.001 PHE C 63 TYR 0.008 0.001 TYR L 50 ARG 0.001 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.344 Fit side-chains revert: symmetry clash REVERT: E 346 ARG cc_start: 0.7501 (ttp80) cc_final: 0.7247 (ptm-80) outliers start: 10 outliers final: 10 residues processed: 68 average time/residue: 0.1253 time to fit residues: 10.8044 Evaluate side-chains 65 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.0870 chunk 25 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 41 optimal weight: 1.9990 chunk 10 optimal weight: 0.4980 chunk 28 optimal weight: 0.2980 chunk 0 optimal weight: 3.9990 chunk 22 optimal weight: 1.9990 chunk 30 optimal weight: 0.5980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.138799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3449 r_free = 0.3449 target = 0.115091 restraints weight = 4772.418| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3488 r_free = 0.3488 target = 0.118222 restraints weight = 3153.006| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3512 r_free = 0.3512 target = 0.120277 restraints weight = 2319.484| |-----------------------------------------------------------------------------| r_work (final): 0.3516 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7426 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3422 Z= 0.192 Angle : 0.558 5.563 4662 Z= 0.287 Chirality : 0.042 0.156 496 Planarity : 0.004 0.033 604 Dihedral : 4.388 20.600 474 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.07 % Allowed : 13.13 % Favored : 83.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.27 (0.40), residues: 426 helix: -3.06 (0.81), residues: 21 sheet: 0.44 (0.47), residues: 141 loop : -1.45 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.012 0.001 PHE C 107 TYR 0.008 0.001 TYR C 79 ARG 0.001 0.000 ARG E 493 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: E 346 ARG cc_start: 0.7523 (ttp80) cc_final: 0.7269 (ptm-80) outliers start: 11 outliers final: 10 residues processed: 64 average time/residue: 0.1426 time to fit residues: 11.5360 Evaluate side-chains 67 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 71 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 41 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 8 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 13 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 17 optimal weight: 0.0770 chunk 35 optimal weight: 0.9990 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.137435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.113809 restraints weight = 4752.331| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3468 r_free = 0.3468 target = 0.116833 restraints weight = 3141.297| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3494 r_free = 0.3494 target = 0.118951 restraints weight = 2319.069| |-----------------------------------------------------------------------------| r_work (final): 0.3498 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7467 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3422 Z= 0.217 Angle : 0.571 6.130 4662 Z= 0.294 Chirality : 0.042 0.152 496 Planarity : 0.004 0.034 604 Dihedral : 4.445 23.143 474 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 5.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 3.07 % Allowed : 13.41 % Favored : 83.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.33 (0.41), residues: 426 helix: -3.23 (0.79), residues: 21 sheet: 0.21 (0.46), residues: 151 loop : -1.41 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP C 106 HIS 0.003 0.001 HIS E 505 PHE 0.009 0.001 PHE E 374 TYR 0.008 0.001 TYR L 50 ARG 0.001 0.000 ARG E 408 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.369 Fit side-chains REVERT: E 346 ARG cc_start: 0.7496 (ttp80) cc_final: 0.7247 (ptm-80) REVERT: E 417 LYS cc_start: 0.8957 (ttpp) cc_final: 0.8589 (ttpp) outliers start: 11 outliers final: 10 residues processed: 65 average time/residue: 0.1337 time to fit residues: 11.0056 Evaluate side-chains 66 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 56 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Chi-restraints excluded: chain L residue 96 LEU Chi-restraints excluded: chain L residue 110 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.0040 chunk 21 optimal weight: 0.8980 chunk 29 optimal weight: 0.3980 chunk 8 optimal weight: 0.6980 chunk 0 optimal weight: 3.9990 chunk 17 optimal weight: 0.0170 chunk 27 optimal weight: 0.0040 chunk 11 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 14 optimal weight: 0.6980 chunk 34 optimal weight: 3.9990 overall best weight: 0.2242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.140698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.117089 restraints weight = 4643.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.120200 restraints weight = 3047.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.122532 restraints weight = 2233.245| |-----------------------------------------------------------------------------| r_work (final): 0.3546 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7387 moved from start: 0.2090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 3422 Z= 0.167 Angle : 0.551 6.535 4662 Z= 0.284 Chirality : 0.042 0.160 496 Planarity : 0.004 0.034 604 Dihedral : 4.183 19.956 474 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 1.68 % Allowed : 15.92 % Favored : 82.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.20 (0.41), residues: 426 helix: -3.15 (0.84), residues: 21 sheet: 0.49 (0.47), residues: 141 loop : -1.39 (0.36), residues: 264 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.007 0.001 PHE E 400 TYR 0.010 0.001 TYR C 79 ARG 0.001 0.000 ARG C 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 63 time to evaluate : 0.360 Fit side-chains REVERT: E 346 ARG cc_start: 0.7525 (ttp80) cc_final: 0.7249 (ptm-80) REVERT: E 417 LYS cc_start: 0.8898 (ttpp) cc_final: 0.8554 (ttpp) outliers start: 6 outliers final: 6 residues processed: 67 average time/residue: 0.1472 time to fit residues: 12.2279 Evaluate side-chains 64 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 58 time to evaluate : 0.364 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 3.9990 chunk 1 optimal weight: 0.0670 chunk 38 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.137665 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3442 r_free = 0.3442 target = 0.114443 restraints weight = 4720.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3478 r_free = 0.3478 target = 0.117319 restraints weight = 3133.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3506 r_free = 0.3506 target = 0.119493 restraints weight = 2328.277| |-----------------------------------------------------------------------------| r_work (final): 0.3509 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7455 moved from start: 0.2125 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3422 Z= 0.224 Angle : 0.587 5.933 4662 Z= 0.307 Chirality : 0.043 0.152 496 Planarity : 0.004 0.035 604 Dihedral : 4.347 22.433 474 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 5.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.57 % Favored : 93.43 % Rotamer: Outliers : 2.51 % Allowed : 16.76 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.41), residues: 426 helix: -3.26 (0.80), residues: 21 sheet: 0.24 (0.46), residues: 152 loop : -1.40 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP C 106 HIS 0.002 0.001 HIS E 505 PHE 0.012 0.001 PHE C 63 TYR 0.007 0.001 TYR E 423 ARG 0.002 0.000 ARG E 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 58 time to evaluate : 0.338 Fit side-chains REVERT: E 346 ARG cc_start: 0.7506 (ttp80) cc_final: 0.7252 (ptm-80) REVERT: E 417 LYS cc_start: 0.8975 (ttpp) cc_final: 0.8609 (ttpp) outliers start: 9 outliers final: 8 residues processed: 65 average time/residue: 0.1293 time to fit residues: 10.7462 Evaluate side-chains 66 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.333 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 30 THR Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 37 optimal weight: 0.1980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 11 optimal weight: 0.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 13 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.137292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.114037 restraints weight = 4649.549| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.3475 r_free = 0.3475 target = 0.116887 restraints weight = 3134.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.118996 restraints weight = 2336.469| |-----------------------------------------------------------------------------| r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7459 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3422 Z= 0.215 Angle : 0.585 5.396 4662 Z= 0.308 Chirality : 0.043 0.152 496 Planarity : 0.004 0.037 604 Dihedral : 4.432 24.468 474 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 1.96 % Allowed : 17.88 % Favored : 80.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.41), residues: 426 helix: -3.23 (0.81), residues: 21 sheet: 0.24 (0.46), residues: 152 loop : -1.40 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP C 106 HIS 0.002 0.001 HIS C 35 PHE 0.010 0.001 PHE E 374 TYR 0.009 0.001 TYR C 79 ARG 0.002 0.000 ARG C 86 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 852 Ramachandran restraints generated. 426 Oldfield, 0 Emsley, 426 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 61 time to evaluate : 0.382 Fit side-chains REVERT: E 346 ARG cc_start: 0.7492 (ttp80) cc_final: 0.7244 (ptm-80) REVERT: E 417 LYS cc_start: 0.8952 (ttpp) cc_final: 0.8536 (ttpp) outliers start: 7 outliers final: 7 residues processed: 67 average time/residue: 0.1311 time to fit residues: 11.1545 Evaluate side-chains 65 residues out of total 362 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 58 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 2 VAL Chi-restraints excluded: chain C residue 114 THR Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 512 VAL Chi-restraints excluded: chain E residue 524 VAL Chi-restraints excluded: chain E residue 525 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 19 optimal weight: 0.8980 chunk 34 optimal weight: 0.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 39 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 20 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.134754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.111709 restraints weight = 4709.811| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3441 r_free = 0.3441 target = 0.114551 restraints weight = 3089.224| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3470 r_free = 0.3470 target = 0.116742 restraints weight = 2275.258| |-----------------------------------------------------------------------------| r_work (final): 0.3465 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7513 moved from start: 0.2258 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 3422 Z= 0.269 Angle : 0.630 5.436 4662 Z= 0.332 Chirality : 0.043 0.144 496 Planarity : 0.004 0.036 604 Dihedral : 4.709 27.247 474 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 2.79 % Allowed : 16.48 % Favored : 80.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.38 (0.41), residues: 426 helix: -3.27 (0.80), residues: 21 sheet: 0.18 (0.46), residues: 150 loop : -1.44 (0.37), residues: 255 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP C 106 HIS 0.003 0.001 HIS E 505 PHE 0.012 0.002 PHE E 429 TYR 0.008 0.001 TYR L 50 ARG 0.003 0.000 ARG C 66 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1722.07 seconds wall clock time: 30 minutes 40.18 seconds (1840.18 seconds total)