Starting phenix.real_space_refine on Wed Mar 5 19:27:10 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dpz_27644/03_2025/8dpz_27644.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dpz_27644/03_2025/8dpz_27644.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.38 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dpz_27644/03_2025/8dpz_27644.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dpz_27644/03_2025/8dpz_27644.map" model { file = "/net/cci-nas-00/data/ceres_data/8dpz_27644/03_2025/8dpz_27644.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dpz_27644/03_2025/8dpz_27644.cif" } resolution = 3.38 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= -0.017 sd= 0.107 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 11 5.16 5 C 2115 2.51 5 N 551 2.21 5 O 649 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 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: 3326 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 1480 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1480 Classifications: {'peptide': 185} Link IDs: {'PTRANS': 10, 'TRANS': 174} Chain breaks: 1 Chain: "F" Number of atoms: 982 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 982 Classifications: {'peptide': 128} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 5, 'TRANS': 122} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 7, 'TRANS': 99} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 6 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.07, per 1000 atoms: 0.92 Number of scatterers: 3326 At special positions: 0 Unit cell: (71.28, 90.72, 74.52, 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 11 16.00 O 649 8.00 N 551 7.00 C 2115 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.03 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS F 22 " - pdb=" SG CYS F 92 " distance=2.03 Simple disulfide: pdb=" SG CYS G 23 " - pdb=" SG CYS G 88 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN B 343 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 430.3 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 770 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 6 sheets defined 11.2% alpha, 39.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'B' and resid 337 through 343 Processing helix chain 'B' and resid 364 through 370 removed outlier: 4.210A pdb=" N LEU B 368 " --> pdb=" O ASP B 364 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 390 removed outlier: 3.822A pdb=" N ASN B 388 " --> pdb=" O THR B 385 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N LEU B 390 " --> pdb=" O LEU B 387 " (cutoff:3.500A) Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 removed outlier: 3.608A pdb=" N SER B 443 " --> pdb=" O ASN B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'F' and resid 83 through 87 removed outlier: 3.959A pdb=" N THR F 87 " --> pdb=" O ALA F 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 354 through 358 removed outlier: 3.535A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) removed outlier: 10.918A pdb=" N GLU F 100H" --> pdb=" O TYR F 98 " (cutoff:3.500A) removed outlier: 12.269A pdb=" N TYR F 98 " --> pdb=" O GLU F 100H" (cutoff:3.500A) removed outlier: 6.147A pdb=" N ALA F 100J" --> pdb=" O ALA F 96 " (cutoff:3.500A) removed outlier: 6.703A pdb=" N ARG F 94 " --> pdb=" O ASP F 101 " (cutoff:3.500A) removed outlier: 4.651A pdb=" N TRP F 103 " --> pdb=" O CYS F 92 " (cutoff:3.500A) removed outlier: 6.599A pdb=" N CYS F 92 " --> pdb=" O TRP F 103 " (cutoff:3.500A) removed outlier: 4.812A pdb=" N ASN F 33 " --> pdb=" O VAL F 95 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N GLY F 49 " --> pdb=" O TRP F 36 " (cutoff:3.500A) removed outlier: 6.315A pdb=" N ARG F 38 " --> pdb=" O TRP F 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP F 47 " --> pdb=" O ARG F 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'F' and resid 3 through 7 removed outlier: 3.623A pdb=" N GLN F 5 " --> pdb=" O ALA F 23 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'G' and resid 4 through 5 Processing sheet with id=AA6, first strand: chain 'G' and resid 10 through 13 removed outlier: 3.536A pdb=" N ALA G 34 " --> pdb=" O GLN G 89 " (cutoff:3.500A) removed outlier: 6.740A pdb=" N VAL G 33 " --> pdb=" O TYR G 49 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N TYR G 49 " --> pdb=" O VAL G 33 " (cutoff:3.500A) removed outlier: 6.497A pdb=" N TRP G 35 " --> pdb=" O LEU G 47 " (cutoff:3.500A) 129 hydrogen bonds defined for protein. 324 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: 0.98 Time building geometry restraints manager: 1.12 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1045 1.34 - 1.46: 898 1.46 - 1.58: 1458 1.58 - 1.70: 0 1.70 - 1.81: 12 Bond restraints: 3413 Sorted by residual: bond pdb=" C GLU G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.334 1.351 -0.018 8.40e-03 1.42e+04 4.43e+00 bond pdb=" C1 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.02e+00 bond pdb=" C SER G 7 " pdb=" N PRO G 8 " ideal model delta sigma weight residual 1.334 1.376 -0.042 2.34e-02 1.83e+03 3.27e+00 bond pdb=" C1 NAG A 1 " pdb=" O5 NAG A 1 " ideal model delta sigma weight residual 1.406 1.440 -0.034 2.00e-02 2.50e+03 2.83e+00 bond pdb=" CB ASP F 100A" pdb=" CG ASP F 100A" ideal model delta sigma weight residual 1.516 1.549 -0.033 2.50e-02 1.60e+03 1.70e+00 ... (remaining 3408 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.63: 4413 1.63 - 3.26: 188 3.26 - 4.89: 31 4.89 - 6.51: 7 6.51 - 8.14: 3 Bond angle restraints: 4642 Sorted by residual: angle pdb=" C ASP G 50 " pdb=" N ALA G 51 " pdb=" CA ALA G 51 " ideal model delta sigma weight residual 121.54 127.36 -5.82 1.91e+00 2.74e-01 9.29e+00 angle pdb=" N ASP F 100 " pdb=" CA ASP F 100 " pdb=" C ASP F 100 " ideal model delta sigma weight residual 109.95 105.91 4.04 1.44e+00 4.82e-01 7.86e+00 angle pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta sigma weight residual 120.06 123.39 -3.33 1.19e+00 7.06e-01 7.81e+00 angle pdb=" C PHE G 83 " pdb=" CA PHE G 83 " pdb=" CB PHE G 83 " ideal model delta sigma weight residual 111.31 115.81 -4.50 1.68e+00 3.54e-01 7.18e+00 angle pdb=" N TRP G 94 " pdb=" CA TRP G 94 " pdb=" C TRP G 94 " ideal model delta sigma weight residual 113.57 117.12 -3.55 1.38e+00 5.25e-01 6.62e+00 ... (remaining 4637 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.50: 1822 16.50 - 33.01: 177 33.01 - 49.51: 25 49.51 - 66.02: 5 66.02 - 82.52: 4 Dihedral angle restraints: 2033 sinusoidal: 817 harmonic: 1216 Sorted by residual: dihedral pdb=" CB CYS F 22 " pdb=" SG CYS F 22 " pdb=" SG CYS F 92 " pdb=" CB CYS F 92 " ideal model delta sinusoidal sigma weight residual 93.00 56.65 36.35 1 1.00e+01 1.00e-02 1.87e+01 dihedral pdb=" CA VAL F 95 " pdb=" C VAL F 95 " pdb=" N ALA F 96 " pdb=" CA ALA F 96 " ideal model delta harmonic sigma weight residual 180.00 -161.57 -18.43 0 5.00e+00 4.00e-02 1.36e+01 dihedral pdb=" CA ASN G 93 " pdb=" C ASN G 93 " pdb=" N TRP G 94 " pdb=" CA TRP G 94 " ideal model delta harmonic sigma weight residual -180.00 -161.85 -18.15 0 5.00e+00 4.00e-02 1.32e+01 ... (remaining 2030 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 290 0.035 - 0.070: 137 0.070 - 0.106: 51 0.106 - 0.141: 19 0.141 - 0.176: 4 Chirality restraints: 501 Sorted by residual: chirality pdb=" CB THR G 102 " pdb=" CA THR G 102 " pdb=" OG1 THR G 102 " pdb=" CG2 THR G 102 " both_signs ideal model delta sigma weight residual False 2.55 2.38 0.18 2.00e-01 2.50e+01 7.76e-01 chirality pdb=" CA TRP G 94 " pdb=" N TRP G 94 " pdb=" C TRP G 94 " pdb=" CB TRP G 94 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.73e-01 chirality pdb=" CA ILE B 402 " pdb=" N ILE B 402 " pdb=" C ILE B 402 " pdb=" CB ILE B 402 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.47e-01 ... (remaining 498 not shown) Planarity restraints: 596 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU G 79 " -0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO G 80 " 0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.036 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C CYS B 336 " 0.041 5.00e-02 4.00e+02 6.29e-02 6.34e+00 pdb=" N PRO B 337 " -0.109 5.00e-02 4.00e+02 pdb=" CA PRO B 337 " 0.032 5.00e-02 4.00e+02 pdb=" CD PRO B 337 " 0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE G 83 " -0.014 2.00e-02 2.50e+03 1.57e-02 4.33e+00 pdb=" CG PHE G 83 " 0.037 2.00e-02 2.50e+03 pdb=" CD1 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE G 83 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE G 83 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE G 83 " -0.001 2.00e-02 2.50e+03 ... (remaining 593 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1186 2.87 - 3.38: 2663 3.38 - 3.89: 5282 3.89 - 4.39: 5920 4.39 - 4.90: 10828 Nonbonded interactions: 25879 Sorted by model distance: nonbonded pdb=" OH TYR F 97 " pdb=" OE1 GLU F 99 " model vdw 2.363 3.040 nonbonded pdb=" OD2 ASP B 405 " pdb=" OG SER G 30 " model vdw 2.408 3.040 nonbonded pdb=" NH1 ARG B 457 " pdb=" OD2 ASP B 467 " model vdw 2.420 3.120 nonbonded pdb=" OD1 ASP F 100 " pdb=" N ASP F 100A" model vdw 2.427 3.120 nonbonded pdb=" NH1 ARG G 61 " pdb=" OD2 ASP G 82 " model vdw 2.429 3.120 ... (remaining 25874 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.890 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: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 14.510 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:3.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 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 : 0.004 0.042 3413 Z= 0.260 Angle : 0.772 8.142 4642 Z= 0.412 Chirality : 0.050 0.176 501 Planarity : 0.007 0.069 595 Dihedral : 13.012 82.522 1248 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 1.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.00 % Allowed : 0.28 % Favored : 99.72 % 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: -2.09 (0.38), residues: 412 helix: -4.20 (0.35), residues: 27 sheet: -0.08 (0.45), residues: 139 loop : -1.92 (0.35), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP F 103 HIS 0.001 0.001 HIS B 519 PHE 0.037 0.003 PHE G 83 TYR 0.018 0.002 TYR G 49 ARG 0.006 0.001 ARG G 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.358 Fit side-chains REVERT: B 406 GLU cc_start: 0.8205 (mt-10) cc_final: 0.7919 (mt-10) REVERT: B 417 LYS cc_start: 0.8402 (tppt) cc_final: 0.8171 (tptt) REVERT: F 48 ILE cc_start: 0.8306 (mm) cc_final: 0.7982 (mm) outliers start: 0 outliers final: 0 residues processed: 65 average time/residue: 0.2095 time to fit residues: 15.9214 Evaluate side-chains 55 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 11 optimal weight: 0.0010 overall best weight: 0.8388 ------------------------------------------------------------------------------- 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 = 0.3541 r_free = 0.3541 target = 0.118392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.099165 restraints weight = 5075.201| |-----------------------------------------------------------------------------| r_work (start): 0.3271 rms_B_bonded: 2.18 r_work: 0.3163 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3035 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3035 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8166 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 3413 Z= 0.266 Angle : 0.601 5.182 4642 Z= 0.320 Chirality : 0.045 0.158 501 Planarity : 0.005 0.053 595 Dihedral : 5.245 25.055 510 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.28 % Allowed : 6.39 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.63 (0.40), residues: 412 helix: -3.73 (0.53), residues: 28 sheet: 0.26 (0.47), residues: 140 loop : -1.63 (0.36), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.023 0.002 PHE G 83 TYR 0.012 0.001 TYR B 453 ARG 0.003 0.001 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 59 time to evaluate : 0.361 Fit side-chains REVERT: B 417 LYS cc_start: 0.8621 (tppt) cc_final: 0.8348 (tptt) REVERT: F 48 ILE cc_start: 0.8551 (mm) cc_final: 0.8312 (mm) REVERT: F 58 ASP cc_start: 0.8312 (t0) cc_final: 0.8105 (t0) REVERT: F 100 GLU cc_start: 0.8194 (tm-30) cc_final: 0.7822 (tm-30) outliers start: 1 outliers final: 1 residues processed: 59 average time/residue: 0.2182 time to fit residues: 15.0037 Evaluate side-chains 57 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 56 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 6 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 30 optimal weight: 0.9980 chunk 36 optimal weight: 0.6980 chunk 25 optimal weight: 1.9990 chunk 5 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3545 r_free = 0.3545 target = 0.118497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.099510 restraints weight = 5016.500| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.15 r_work: 0.3169 rms_B_bonded: 2.46 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1578 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3413 Z= 0.197 Angle : 0.553 5.198 4642 Z= 0.290 Chirality : 0.045 0.163 501 Planarity : 0.004 0.049 595 Dihedral : 4.904 22.173 510 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.64 % Favored : 96.36 % Rotamer: Outliers : 0.56 % Allowed : 9.44 % Favored : 90.00 % 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: -1.43 (0.40), residues: 412 helix: -3.27 (0.68), residues: 28 sheet: 0.19 (0.45), residues: 148 loop : -1.44 (0.37), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.018 0.002 PHE G 83 TYR 0.013 0.001 TYR F 100F ARG 0.003 0.000 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 59 time to evaluate : 0.390 Fit side-chains REVERT: B 417 LYS cc_start: 0.8642 (tppt) cc_final: 0.8267 (tppt) REVERT: B 418 ILE cc_start: 0.8284 (OUTLIER) cc_final: 0.7898 (mt) REVERT: F 48 ILE cc_start: 0.8533 (mm) cc_final: 0.8333 (mm) REVERT: F 100 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7656 (tm-30) outliers start: 2 outliers final: 0 residues processed: 60 average time/residue: 0.2248 time to fit residues: 15.8081 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 418 ILE Chi-restraints excluded: chain F residue 100 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.6980 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 32 optimal weight: 0.1980 chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 5 optimal weight: 0.0770 chunk 39 optimal weight: 0.8980 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 0.0970 overall best weight: 0.3936 ------------------------------------------------------------------------------- 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 = 0.3568 r_free = 0.3568 target = 0.120178 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.100630 restraints weight = 5095.519| |-----------------------------------------------------------------------------| r_work (start): 0.3297 rms_B_bonded: 2.26 r_work: 0.3188 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3058 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8106 moved from start: 0.1697 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3413 Z= 0.167 Angle : 0.561 11.318 4642 Z= 0.292 Chirality : 0.045 0.148 501 Planarity : 0.004 0.047 595 Dihedral : 4.715 20.201 510 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 3.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 1.11 % Allowed : 10.56 % Favored : 88.33 % 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: 412 helix: -2.60 (0.91), residues: 21 sheet: 0.27 (0.45), residues: 148 loop : -1.48 (0.37), residues: 243 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 94 HIS 0.000 0.000 HIS B 519 PHE 0.016 0.002 PHE G 83 TYR 0.014 0.001 TYR F 100F ARG 0.002 0.000 ARG G 18 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.402 Fit side-chains REVERT: B 417 LYS cc_start: 0.8626 (tppt) cc_final: 0.8256 (tppt) REVERT: F 99 GLU cc_start: 0.8955 (tt0) cc_final: 0.8704 (tt0) REVERT: F 100 GLU cc_start: 0.8055 (OUTLIER) cc_final: 0.7540 (tm-30) outliers start: 4 outliers final: 2 residues processed: 60 average time/residue: 0.2219 time to fit residues: 15.6561 Evaluate side-chains 60 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.405 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.4980 chunk 21 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 34 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 29 optimal weight: 0.7980 chunk 0 optimal weight: 0.5980 chunk 35 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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 = 0.3539 r_free = 0.3539 target = 0.118323 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.098676 restraints weight = 5092.632| |-----------------------------------------------------------------------------| r_work (start): 0.3265 rms_B_bonded: 2.26 r_work: 0.3154 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3025 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.3025 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8137 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3413 Z= 0.235 Angle : 0.590 10.221 4642 Z= 0.305 Chirality : 0.046 0.162 501 Planarity : 0.004 0.044 595 Dihedral : 4.787 20.754 510 Min Nonbonded Distance : 2.572 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer: Outliers : 3.06 % Allowed : 9.72 % Favored : 87.22 % 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: -1.28 (0.40), residues: 412 helix: -2.74 (0.84), residues: 27 sheet: 0.23 (0.45), residues: 148 loop : -1.36 (0.38), residues: 237 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.017 0.002 PHE F 78 TYR 0.015 0.001 TYR F 100F ARG 0.002 0.000 ARG G 18 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 58 time to evaluate : 0.394 Fit side-chains REVERT: B 347 PHE cc_start: 0.8769 (OUTLIER) cc_final: 0.7697 (m-10) REVERT: B 417 LYS cc_start: 0.8649 (tppt) cc_final: 0.8252 (tppt) REVERT: F 100 GLU cc_start: 0.8151 (OUTLIER) cc_final: 0.7631 (tm-30) outliers start: 11 outliers final: 5 residues processed: 64 average time/residue: 0.2119 time to fit residues: 16.0213 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 6 optimal weight: 0.9990 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 9 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 overall best weight: 0.9186 ------------------------------------------------------------------------------- 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 = 0.3525 r_free = 0.3525 target = 0.117404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.097649 restraints weight = 5231.457| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 2.26 r_work: 0.3138 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.2063 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3413 Z= 0.288 Angle : 0.622 9.458 4642 Z= 0.322 Chirality : 0.047 0.173 501 Planarity : 0.004 0.043 595 Dihedral : 4.979 21.365 510 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 2.78 % Allowed : 12.22 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.50 (0.40), residues: 412 helix: -2.58 (0.97), residues: 21 sheet: -0.05 (0.47), residues: 135 loop : -1.44 (0.36), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 94 HIS 0.001 0.001 HIS B 519 PHE 0.018 0.002 PHE F 78 TYR 0.017 0.001 TYR F 100F ARG 0.004 0.000 ARG G 18 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.396 Fit side-chains REVERT: B 347 PHE cc_start: 0.8792 (OUTLIER) cc_final: 0.7759 (m-10) REVERT: B 376 THR cc_start: 0.9077 (OUTLIER) cc_final: 0.8723 (p) REVERT: B 417 LYS cc_start: 0.8648 (tppt) cc_final: 0.8228 (tppt) REVERT: F 100 GLU cc_start: 0.8247 (OUTLIER) cc_final: 0.7762 (tm-30) outliers start: 10 outliers final: 4 residues processed: 60 average time/residue: 0.1894 time to fit residues: 13.7124 Evaluate side-chains 62 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 4.9990 chunk 23 optimal weight: 0.9990 chunk 28 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 1.9990 chunk 36 optimal weight: 0.8980 chunk 14 optimal weight: 3.9990 chunk 7 optimal weight: 0.3980 chunk 33 optimal weight: 0.9990 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3536 r_free = 0.3536 target = 0.118099 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.098363 restraints weight = 5089.007| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.25 r_work: 0.3149 rms_B_bonded: 2.53 restraints_weight: 0.5000 r_work: 0.3026 rms_B_bonded: 4.14 restraints_weight: 0.2500 r_work (final): 0.3026 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 3413 Z= 0.243 Angle : 0.604 8.762 4642 Z= 0.314 Chirality : 0.046 0.167 501 Planarity : 0.004 0.044 595 Dihedral : 4.950 20.637 510 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.37 % Favored : 95.63 % Rotamer: Outliers : 3.06 % Allowed : 11.94 % Favored : 85.00 % 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: -1.56 (0.39), residues: 412 helix: -2.54 (0.97), residues: 21 sheet: -0.10 (0.46), residues: 135 loop : -1.47 (0.35), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.002 PHE F 78 TYR 0.019 0.001 TYR F 100F ARG 0.003 0.000 ARG G 18 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.358 Fit side-chains REVERT: B 347 PHE cc_start: 0.8753 (OUTLIER) cc_final: 0.7713 (m-10) REVERT: B 376 THR cc_start: 0.9069 (OUTLIER) cc_final: 0.8717 (p) REVERT: B 417 LYS cc_start: 0.8640 (tppt) cc_final: 0.8301 (tptt) REVERT: F 82 LEU cc_start: 0.8156 (OUTLIER) cc_final: 0.7727 (mp) REVERT: F 100 GLU cc_start: 0.8206 (OUTLIER) cc_final: 0.7689 (tm-30) outliers start: 11 outliers final: 5 residues processed: 64 average time/residue: 0.1848 time to fit residues: 14.1976 Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.391 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 21 THR Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 3 optimal weight: 0.5980 chunk 10 optimal weight: 0.4980 chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 0.0010 chunk 34 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 overall best weight: 0.4786 ------------------------------------------------------------------------------- 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 = 0.3557 r_free = 0.3557 target = 0.119716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.100021 restraints weight = 5075.124| |-----------------------------------------------------------------------------| r_work (start): 0.3280 rms_B_bonded: 2.26 r_work: 0.3172 rms_B_bonded: 2.52 restraints_weight: 0.5000 r_work: 0.3042 rms_B_bonded: 4.20 restraints_weight: 0.2500 r_work (final): 0.3042 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8109 moved from start: 0.2152 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3413 Z= 0.184 Angle : 0.573 8.017 4642 Z= 0.296 Chirality : 0.045 0.152 501 Planarity : 0.004 0.044 595 Dihedral : 4.760 19.976 510 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.22 % Allowed : 13.89 % Favored : 83.89 % 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: -1.42 (0.40), residues: 412 helix: -2.18 (1.22), residues: 15 sheet: -0.24 (0.46), residues: 143 loop : -1.32 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.015 0.001 PHE F 78 TYR 0.017 0.001 TYR F 100F ARG 0.002 0.000 ARG F 50 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 53 time to evaluate : 0.385 Fit side-chains REVERT: B 347 PHE cc_start: 0.8702 (OUTLIER) cc_final: 0.7514 (m-10) REVERT: B 417 LYS cc_start: 0.8601 (tppt) cc_final: 0.8253 (tptt) REVERT: F 82 LEU cc_start: 0.8103 (OUTLIER) cc_final: 0.7664 (mp) REVERT: F 100 GLU cc_start: 0.8146 (OUTLIER) cc_final: 0.7545 (tm-30) outliers start: 8 outliers final: 4 residues processed: 59 average time/residue: 0.2025 time to fit residues: 14.3721 Evaluate side-chains 59 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 8.9990 chunk 24 optimal weight: 0.1980 chunk 28 optimal weight: 0.6980 chunk 11 optimal weight: 0.7980 chunk 3 optimal weight: 0.4980 chunk 16 optimal weight: 0.9980 chunk 2 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.3559 r_free = 0.3559 target = 0.119813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.099666 restraints weight = 5060.571| |-----------------------------------------------------------------------------| r_work (start): 0.3281 rms_B_bonded: 2.34 r_work: 0.3167 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3041 rms_B_bonded: 4.35 restraints_weight: 0.2500 r_work (final): 0.3041 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2253 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3413 Z= 0.199 Angle : 0.587 7.891 4642 Z= 0.300 Chirality : 0.045 0.151 501 Planarity : 0.004 0.044 595 Dihedral : 4.727 19.964 510 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.50 % Allowed : 13.61 % Favored : 83.89 % 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: -1.35 (0.40), residues: 412 helix: -2.00 (1.27), residues: 15 sheet: -0.21 (0.46), residues: 143 loop : -1.26 (0.36), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.015 0.001 PHE F 78 TYR 0.024 0.001 TYR F 59 ARG 0.001 0.000 ARG G 18 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 56 time to evaluate : 0.393 Fit side-chains REVERT: B 347 PHE cc_start: 0.8703 (OUTLIER) cc_final: 0.7476 (m-10) REVERT: B 376 THR cc_start: 0.9002 (OUTLIER) cc_final: 0.8688 (p) REVERT: B 417 LYS cc_start: 0.8581 (tppt) cc_final: 0.8230 (tptt) REVERT: F 82 LEU cc_start: 0.8078 (OUTLIER) cc_final: 0.7679 (mp) REVERT: F 100 ASP cc_start: 0.8572 (t0) cc_final: 0.8307 (t0) REVERT: F 100 GLU cc_start: 0.8197 (OUTLIER) cc_final: 0.7595 (tm-30) outliers start: 9 outliers final: 3 residues processed: 63 average time/residue: 0.1950 time to fit residues: 14.5705 Evaluate side-chains 61 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 54 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 26 optimal weight: 2.9990 chunk 15 optimal weight: 0.0040 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.5980 chunk 7 optimal weight: 0.7980 chunk 28 optimal weight: 0.8980 chunk 2 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5392 ------------------------------------------------------------------------------- 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 = 0.3556 r_free = 0.3556 target = 0.119906 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.100221 restraints weight = 5037.481| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.24 r_work: 0.3174 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.3044 rms_B_bonded: 4.28 restraints_weight: 0.2500 r_work (final): 0.3044 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8116 moved from start: 0.2348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3413 Z= 0.202 Angle : 0.587 8.160 4642 Z= 0.299 Chirality : 0.045 0.151 501 Planarity : 0.004 0.044 595 Dihedral : 4.692 20.918 510 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 2.50 % Allowed : 13.33 % Favored : 84.17 % 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: -1.22 (0.40), residues: 412 helix: -1.93 (1.28), residues: 15 sheet: 0.06 (0.47), residues: 137 loop : -1.27 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.016 0.001 PHE F 78 TYR 0.015 0.001 TYR F 100F ARG 0.002 0.000 ARG G 18 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.395 Fit side-chains REVERT: B 347 PHE cc_start: 0.8718 (OUTLIER) cc_final: 0.7531 (m-10) REVERT: B 376 THR cc_start: 0.9046 (OUTLIER) cc_final: 0.8725 (p) REVERT: B 417 LYS cc_start: 0.8614 (tppt) cc_final: 0.8264 (tptt) REVERT: F 82 LEU cc_start: 0.8177 (OUTLIER) cc_final: 0.7884 (mp) REVERT: F 100 GLU cc_start: 0.8223 (OUTLIER) cc_final: 0.7650 (tm-30) outliers start: 9 outliers final: 4 residues processed: 61 average time/residue: 0.2076 time to fit residues: 15.0866 Evaluate side-chains 63 residues out of total 360 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.388 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 347 PHE Chi-restraints excluded: chain B residue 376 THR Chi-restraints excluded: chain B residue 510 VAL Chi-restraints excluded: chain F residue 68 THR Chi-restraints excluded: chain F residue 82 LEU Chi-restraints excluded: chain F residue 83 THR Chi-restraints excluded: chain F residue 100 GLU Chi-restraints excluded: chain G residue 46 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 3.9990 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 3 optimal weight: 0.6980 chunk 23 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 28 optimal weight: 0.2980 chunk 31 optimal weight: 5.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 = 0.3561 r_free = 0.3561 target = 0.120331 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.101046 restraints weight = 5087.683| |-----------------------------------------------------------------------------| r_work (start): 0.3298 rms_B_bonded: 2.16 r_work: 0.3188 rms_B_bonded: 2.48 restraints_weight: 0.5000 r_work: 0.3061 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.3061 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8123 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3413 Z= 0.193 Angle : 0.581 8.383 4642 Z= 0.295 Chirality : 0.045 0.148 501 Planarity : 0.004 0.044 595 Dihedral : 4.712 22.823 510 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer: Outliers : 2.50 % Allowed : 13.33 % Favored : 84.17 % 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: -1.17 (0.40), residues: 412 helix: -1.82 (1.32), residues: 15 sheet: 0.07 (0.47), residues: 137 loop : -1.22 (0.36), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP G 94 HIS 0.001 0.000 HIS B 519 PHE 0.015 0.001 PHE F 78 TYR 0.025 0.001 TYR F 59 ARG 0.002 0.000 ARG G 18 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2473.16 seconds wall clock time: 43 minutes 3.21 seconds (2583.21 seconds total)