Starting phenix.real_space_refine on Wed Mar 5 22:16:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mkm_23899/03_2025/7mkm_23899.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mkm_23899/03_2025/7mkm_23899.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mkm_23899/03_2025/7mkm_23899.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mkm_23899/03_2025/7mkm_23899.map" model { file = "/net/cci-nas-00/data/ceres_data/7mkm_23899/03_2025/7mkm_23899.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mkm_23899/03_2025/7mkm_23899.cif" } resolution = 3.16 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.017 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 751 atoms to isotropic. 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 17 5.16 5 C 2030 2.51 5 N 528 2.21 5 O 617 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: 3192 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1500 Number of conformers: 1 Conformer: "" Number of residues, atoms: 188, 1500 Classifications: {'peptide': 188} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 178} Chain: "H" Number of atoms: 878 Number of conformers: 1 Conformer: "" Number of residues, atoms: 113, 878 Classifications: {'peptide': 113} Link IDs: {'PTRANS': 4, 'TRANS': 108} Chain: "L" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 800 Classifications: {'peptide': 105} Link IDs: {'PCIS': 1, 'PTRANS': 6, 'TRANS': 97} Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.70, per 1000 atoms: 0.85 Number of scatterers: 3192 At special positions: 0 Unit cell: (77.72, 67.28, 98.6, 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 17 16.00 O 617 8.00 N 528 7.00 C 2030 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.04 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 NAG-ASN " NAG A 601 " - " ASN A 343 " Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 374.8 milliseconds 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 744 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 7 sheets defined 11.1% alpha, 23.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 372 Processing helix chain 'A' and resid 404 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'H' and resid 84 through 89 Processing helix chain 'L' and resid 48 through 52 removed outlier: 3.810A pdb=" N ASN L 52 " --> pdb=" O ASP L 49 " (cutoff:3.500A) Processing helix chain 'L' and resid 78 through 83 Processing sheet with id=AA1, first strand: chain 'A' and resid 355 through 358 removed outlier: 4.100A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) removed outlier: 3.740A pdb=" N TYR A 396 " --> pdb=" O SER A 514 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N SER A 514 " --> pdb=" O TYR A 396 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N LEU A 513 " --> pdb=" O CYS A 432 " (cutoff:3.500A) removed outlier: 3.673A pdb=" N CYS A 432 " --> pdb=" O LEU A 513 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.734A pdb=" N LEU H 18 " --> pdb=" O MET H 82 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N MET H 82 " --> pdb=" O LEU H 18 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N ILE H 20 " --> pdb=" O LEU H 80 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLN H 77 " --> pdb=" O ASP H 72 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 46 through 48 removed outlier: 3.607A pdb=" N GLY H 33 " --> pdb=" O ASP H 98 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N VAL H 37 " --> pdb=" O TYR H 94 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N GLN H 39 " --> pdb=" O LYS H 92 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N LYS H 92 " --> pdb=" O GLN H 39 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N TYR H 105 " --> pdb=" O ARG H 97 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 3 through 5 removed outlier: 3.771A pdb=" N VAL L 19 " --> pdb=" O ILE L 74 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N ILE L 74 " --> pdb=" O VAL L 19 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N MET L 21 " --> pdb=" O LEU L 72 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU L 72 " --> pdb=" O MET L 21 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N CYS L 23 " --> pdb=" O TYR L 70 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N TYR L 71 " --> pdb=" O SER L 64 " (cutoff:3.500A) removed outlier: 3.914A pdb=" N SER L 62 " --> pdb=" O THR L 73 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 45 through 47 removed outlier: 4.688A pdb=" N LEU L 45 " --> pdb=" O GLN L 36 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N GLN L 36 " --> pdb=" O LEU L 45 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N GLN L 88 " --> pdb=" O TYR L 33 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N TYR L 35 " --> pdb=" O TYR L 86 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 198 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: 0.66 Time building geometry restraints manager: 0.79 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: 1009 1.34 - 1.46: 881 1.46 - 1.58: 1364 1.58 - 1.70: 0 1.70 - 1.82: 22 Bond restraints: 3276 Sorted by residual: bond pdb=" C5 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.29e+00 bond pdb=" C1 NAG A 601 " pdb=" O5 NAG A 601 " ideal model delta sigma weight residual 1.406 1.426 -0.020 2.00e-02 2.50e+03 1.05e+00 bond pdb=" C3 NAG A 601 " pdb=" O3 NAG A 601 " ideal model delta sigma weight residual 1.403 1.423 -0.020 2.00e-02 2.50e+03 9.65e-01 bond pdb=" CA MET L 77 " pdb=" CB MET L 77 " ideal model delta sigma weight residual 1.513 1.536 -0.023 2.59e-02 1.49e+03 7.75e-01 bond pdb=" C2 NAG A 601 " pdb=" N2 NAG A 601 " ideal model delta sigma weight residual 1.439 1.454 -0.015 2.00e-02 2.50e+03 5.78e-01 ... (remaining 3271 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.13: 4317 2.13 - 4.25: 132 4.25 - 6.38: 4 6.38 - 8.50: 2 8.50 - 10.63: 2 Bond angle restraints: 4457 Sorted by residual: angle pdb=" C ARG L 76 " pdb=" N MET L 77 " pdb=" CA MET L 77 " ideal model delta sigma weight residual 122.04 130.76 -8.72 2.11e+00 2.25e-01 1.71e+01 angle pdb=" CA ARG L 60 " pdb=" CB ARG L 60 " pdb=" CG ARG L 60 " ideal model delta sigma weight residual 114.10 121.10 -7.00 2.00e+00 2.50e-01 1.23e+01 angle pdb=" CA LEU H 29 " pdb=" CB LEU H 29 " pdb=" CG LEU H 29 " ideal model delta sigma weight residual 116.30 126.93 -10.63 3.50e+00 8.16e-02 9.23e+00 angle pdb=" C LEU H 67 " pdb=" N SER H 68 " pdb=" CA SER H 68 " ideal model delta sigma weight residual 121.62 126.42 -4.80 1.83e+00 2.99e-01 6.87e+00 angle pdb=" C GLY L 65 " pdb=" N CYS L 66 " pdb=" CA CYS L 66 " ideal model delta sigma weight residual 122.59 126.34 -3.75 1.57e+00 4.06e-01 5.70e+00 ... (remaining 4452 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.71: 1753 17.71 - 35.41: 159 35.41 - 53.12: 21 53.12 - 70.82: 0 70.82 - 88.53: 2 Dihedral angle restraints: 1935 sinusoidal: 758 harmonic: 1177 Sorted by residual: dihedral pdb=" CA MET L 77 " pdb=" C MET L 77 " pdb=" N GLU L 78 " pdb=" CA GLU L 78 " ideal model delta harmonic sigma weight residual -180.00 -152.03 -27.97 0 5.00e+00 4.00e-02 3.13e+01 dihedral pdb=" CA TYR H 59 " pdb=" C TYR H 59 " pdb=" N ASN H 60 " pdb=" CA ASN H 60 " ideal model delta harmonic sigma weight residual 180.00 152.05 27.95 0 5.00e+00 4.00e-02 3.12e+01 dihedral pdb=" CA ASP L 81 " pdb=" C ASP L 81 " pdb=" N ALA L 82 " pdb=" CA ALA L 82 " ideal model delta harmonic sigma weight residual -180.00 -152.57 -27.43 0 5.00e+00 4.00e-02 3.01e+01 ... (remaining 1932 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 312 0.037 - 0.074: 113 0.074 - 0.111: 37 0.111 - 0.147: 16 0.147 - 0.184: 2 Chirality restraints: 480 Sorted by residual: chirality pdb=" CB ILE A 402 " pdb=" CA ILE A 402 " pdb=" CG1 ILE A 402 " pdb=" CG2 ILE A 402 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.49e-01 chirality pdb=" CA ILE L 74 " pdb=" N ILE L 74 " pdb=" C ILE L 74 " pdb=" CB ILE L 74 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.98e-01 chirality pdb=" CA ILE L 47 " pdb=" N ILE L 47 " pdb=" C ILE L 47 " pdb=" CB ILE L 47 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.23e-01 ... (remaining 477 not shown) Planarity restraints: 573 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 490 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.40e+00 pdb=" N PRO A 491 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 491 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 491 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 343 " -0.018 2.00e-02 2.50e+03 1.74e-02 3.80e+00 pdb=" CG ASN A 343 " 0.022 2.00e-02 2.50e+03 pdb=" OD1 ASN A 343 " -0.004 2.00e-02 2.50e+03 pdb=" ND2 ASN A 343 " 0.019 2.00e-02 2.50e+03 pdb=" C1 NAG A 601 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 466 " -0.137 9.50e-02 1.11e+02 6.17e-02 2.96e+00 pdb=" NE ARG A 466 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG A 466 " -0.012 2.00e-02 2.50e+03 pdb=" NH1 ARG A 466 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG A 466 " -0.000 2.00e-02 2.50e+03 ... (remaining 570 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 130 2.72 - 3.27: 3159 3.27 - 3.81: 4603 3.81 - 4.36: 5272 4.36 - 4.90: 9289 Nonbonded interactions: 22453 Sorted by model distance: nonbonded pdb=" O SER H 7 " pdb=" OG1 THR H 21 " model vdw 2.177 3.040 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.274 3.040 nonbonded pdb=" O ASN A 440 " pdb=" ND2 ASN L 91 " model vdw 2.324 3.120 nonbonded pdb=" O ALA A 475 " pdb=" ND2 ASN A 487 " model vdw 2.382 3.120 nonbonded pdb=" OG1 THR A 393 " pdb=" O HIS A 519 " model vdw 2.394 3.040 ... (remaining 22448 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: 1.610 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 11.920 Find NCS groups from input model: 0.030 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:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 16.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5718 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 0.031 3276 Z= 0.171 Angle : 0.795 10.631 4457 Z= 0.432 Chirality : 0.047 0.184 480 Planarity : 0.006 0.062 572 Dihedral : 13.042 88.529 1176 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 7.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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 (0.38), residues: 400 helix: -3.71 (0.45), residues: 32 sheet: 2.48 (0.49), residues: 100 loop : -2.02 (0.31), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 436 HIS 0.002 0.001 HIS H 35 PHE 0.015 0.002 PHE A 429 TYR 0.018 0.003 TYR L 85 ARG 0.014 0.002 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 60 time to evaluate : 0.335 Fit side-chains REVERT: A 486 PHE cc_start: 0.6384 (t80) cc_final: 0.6143 (t80) REVERT: L 34 TRP cc_start: 0.4286 (m100) cc_final: 0.4080 (m100) outliers start: 0 outliers final: 0 residues processed: 60 average time/residue: 0.1633 time to fit residues: 11.9481 Evaluate side-chains 53 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 32 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 10 optimal weight: 0.5980 chunk 19 optimal weight: 0.0050 chunk 15 optimal weight: 0.0970 chunk 30 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 0.8980 chunk 35 optimal weight: 0.9980 overall best weight: 0.2590 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 506 GLN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.201012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4447 r_free = 0.4447 target = 0.178179 restraints weight = 5159.978| |-----------------------------------------------------------------------------| r_work (start): 0.4425 rms_B_bonded: 2.96 r_work: 0.4333 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.4333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5959 moved from start: 0.1839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3276 Z= 0.183 Angle : 0.712 8.035 4457 Z= 0.386 Chirality : 0.046 0.253 480 Planarity : 0.005 0.055 572 Dihedral : 7.501 26.191 471 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 1.15 % Allowed : 10.34 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.08 (0.39), residues: 400 helix: -2.22 (0.89), residues: 26 sheet: 1.56 (0.45), residues: 113 loop : -1.75 (0.34), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 436 HIS 0.001 0.001 HIS H 35 PHE 0.029 0.002 PHE A 400 TYR 0.026 0.002 TYR A 423 ARG 0.002 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 55 time to evaluate : 0.340 Fit side-chains REVERT: A 357 ARG cc_start: 0.7133 (ttt-90) cc_final: 0.6917 (ttt-90) REVERT: A 365 TYR cc_start: 0.6374 (m-80) cc_final: 0.5719 (m-80) REVERT: A 410 ILE cc_start: 0.8259 (OUTLIER) cc_final: 0.7926 (mm) REVERT: A 465 GLU cc_start: 0.6825 (tp30) cc_final: 0.6394 (tp30) REVERT: A 466 ARG cc_start: 0.8013 (mtm-85) cc_final: 0.7323 (mtm-85) REVERT: A 486 PHE cc_start: 0.7038 (t80) cc_final: 0.6546 (t80) outliers start: 4 outliers final: 2 residues processed: 56 average time/residue: 0.1805 time to fit residues: 12.2856 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 14 optimal weight: 0.5980 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 1 optimal weight: 0.5980 chunk 28 optimal weight: 0.0970 chunk 22 optimal weight: 0.0050 chunk 34 optimal weight: 0.9990 chunk 30 optimal weight: 0.0020 chunk 2 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 overall best weight: 0.2600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 35 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.200927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.178111 restraints weight = 5031.401| |-----------------------------------------------------------------------------| r_work (start): 0.4420 rms_B_bonded: 2.99 r_work: 0.4326 rms_B_bonded: 3.38 restraints_weight: 0.5000 r_work (final): 0.4326 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5973 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3276 Z= 0.166 Angle : 0.656 8.328 4457 Z= 0.356 Chirality : 0.045 0.269 480 Planarity : 0.005 0.050 572 Dihedral : 6.730 27.328 471 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 2.59 % Allowed : 12.07 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.09 (0.40), residues: 400 helix: -1.74 (1.04), residues: 26 sheet: 1.24 (0.45), residues: 115 loop : -1.66 (0.35), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 36 HIS 0.000 0.000 HIS A 519 PHE 0.014 0.002 PHE A 400 TYR 0.011 0.001 TYR A 453 ARG 0.001 0.000 ARG L 60 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.350 Fit side-chains REVERT: A 357 ARG cc_start: 0.7278 (ttt-90) cc_final: 0.7008 (ttt-90) REVERT: A 365 TYR cc_start: 0.6464 (m-80) cc_final: 0.5766 (m-80) REVERT: A 410 ILE cc_start: 0.8233 (OUTLIER) cc_final: 0.7869 (mm) REVERT: A 465 GLU cc_start: 0.7012 (tp30) cc_final: 0.6616 (tp30) REVERT: A 486 PHE cc_start: 0.6976 (t80) cc_final: 0.6526 (t80) REVERT: H 82 MET cc_start: -0.1334 (tpp) cc_final: -0.1669 (tpt) outliers start: 9 outliers final: 4 residues processed: 58 average time/residue: 0.1647 time to fit residues: 11.7114 Evaluate side-chains 54 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 410 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain L residue 32 ILE Chi-restraints excluded: chain L residue 41 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 = 0.4571 r_free = 0.4571 target = 0.192314 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.171106 restraints weight = 5156.542| |-----------------------------------------------------------------------------| r_work (start): 0.4356 rms_B_bonded: 2.65 r_work: 0.4267 rms_B_bonded: 3.09 restraints_weight: 0.5000 r_work (final): 0.4267 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6080 moved from start: 0.2823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3276 Z= 0.252 Angle : 0.715 8.522 4457 Z= 0.391 Chirality : 0.047 0.308 480 Planarity : 0.005 0.052 572 Dihedral : 6.954 27.656 471 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.72 % Allowed : 13.79 % Favored : 84.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.57 (0.38), residues: 400 helix: -1.91 (1.02), residues: 26 sheet: 0.51 (0.44), residues: 113 loop : -1.78 (0.35), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP H 47 HIS 0.003 0.002 HIS H 35 PHE 0.013 0.002 PHE A 400 TYR 0.021 0.002 TYR A 423 ARG 0.003 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.315 Fit side-chains REVERT: A 357 ARG cc_start: 0.7300 (ttt-90) cc_final: 0.7080 (ttt-90) REVERT: A 410 ILE cc_start: 0.8386 (mm) cc_final: 0.8018 (mm) REVERT: A 465 GLU cc_start: 0.7092 (tp30) cc_final: 0.6788 (tp30) REVERT: A 486 PHE cc_start: 0.6844 (t80) cc_final: 0.6480 (t80) outliers start: 6 outliers final: 4 residues processed: 54 average time/residue: 0.1573 time to fit residues: 10.3014 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain A residue 452 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 5 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 38 optimal weight: 2.9990 chunk 12 optimal weight: 0.6980 chunk 28 optimal weight: 0.4980 chunk 25 optimal weight: 0.9990 chunk 19 optimal weight: 0.0870 chunk 26 optimal weight: 0.8980 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.7980 overall best weight: 0.4958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN H 1 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4582 r_free = 0.4582 target = 0.193175 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4376 r_free = 0.4376 target = 0.171539 restraints weight = 5167.288| |-----------------------------------------------------------------------------| r_work (start): 0.4364 rms_B_bonded: 2.77 r_work: 0.4268 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.4268 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6082 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3276 Z= 0.205 Angle : 0.665 8.239 4457 Z= 0.363 Chirality : 0.045 0.262 480 Planarity : 0.005 0.052 572 Dihedral : 6.637 27.499 471 Min Nonbonded Distance : 2.545 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.59 % Allowed : 15.23 % Favored : 82.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -1.79 (0.39), residues: 400 helix: -2.02 (1.01), residues: 27 sheet: 0.27 (0.46), residues: 108 loop : -1.86 (0.35), residues: 265 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.013 0.002 PHE A 400 TYR 0.020 0.002 TYR A 423 ARG 0.002 0.000 ARG A 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 48 time to evaluate : 0.341 Fit side-chains REVERT: A 357 ARG cc_start: 0.7354 (ttt-90) cc_final: 0.7119 (ttt-90) REVERT: A 410 ILE cc_start: 0.8316 (mm) cc_final: 0.7973 (mm) REVERT: A 465 GLU cc_start: 0.7042 (tp30) cc_final: 0.6774 (tp30) REVERT: A 466 ARG cc_start: 0.7994 (mtm-85) cc_final: 0.7418 (mtm-85) REVERT: A 486 PHE cc_start: 0.6838 (t80) cc_final: 0.6491 (t80) outliers start: 9 outliers final: 4 residues processed: 55 average time/residue: 0.1724 time to fit residues: 11.5320 Evaluate side-chains 52 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 48 time to evaluate : 0.337 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 35 optimal weight: 1.9990 chunk 19 optimal weight: 0.8980 chunk 1 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 14 optimal weight: 0.8980 chunk 2 optimal weight: 0.8980 chunk 25 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 ASN L 91 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4543 r_free = 0.4543 target = 0.189653 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.168145 restraints weight = 5295.650| |-----------------------------------------------------------------------------| r_work (start): 0.4317 rms_B_bonded: 2.80 r_work: 0.4219 rms_B_bonded: 3.27 restraints_weight: 0.5000 r_work (final): 0.4219 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6183 moved from start: 0.3487 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 3276 Z= 0.299 Angle : 0.743 8.359 4457 Z= 0.407 Chirality : 0.047 0.291 480 Planarity : 0.006 0.054 572 Dihedral : 7.038 27.887 471 Min Nonbonded Distance : 2.527 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.72 % Allowed : 16.67 % Favored : 81.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.20 (0.39), residues: 400 helix: -2.18 (1.01), residues: 27 sheet: -0.21 (0.47), residues: 114 loop : -2.09 (0.34), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP H 36 HIS 0.005 0.002 HIS H 35 PHE 0.015 0.002 PHE A 497 TYR 0.021 0.003 TYR H 58 ARG 0.003 0.001 ARG H 66 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.271 Fit side-chains REVERT: A 357 ARG cc_start: 0.7406 (ttt-90) cc_final: 0.7170 (ttt-90) REVERT: A 410 ILE cc_start: 0.8356 (mm) cc_final: 0.8033 (mm) REVERT: A 465 GLU cc_start: 0.7059 (tp30) cc_final: 0.6836 (tp30) REVERT: A 486 PHE cc_start: 0.6732 (t80) cc_final: 0.6388 (t80) REVERT: A 509 ARG cc_start: 0.7061 (mtt180) cc_final: 0.6114 (mtp85) outliers start: 6 outliers final: 6 residues processed: 58 average time/residue: 0.1650 time to fit residues: 11.5550 Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.309 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 433 VAL Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 12 optimal weight: 0.8980 chunk 22 optimal weight: 0.0050 chunk 11 optimal weight: 0.4980 chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 0.3980 chunk 18 optimal weight: 2.9990 chunk 29 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 overall best weight: 0.4794 ------------------------------------------------------------------------------- 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 = 0.4566 r_free = 0.4566 target = 0.191729 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.170860 restraints weight = 5137.264| |-----------------------------------------------------------------------------| r_work (start): 0.4352 rms_B_bonded: 2.68 r_work: 0.4260 rms_B_bonded: 3.10 restraints_weight: 0.5000 r_work (final): 0.4260 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6118 moved from start: 0.3675 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3276 Z= 0.206 Angle : 0.688 8.058 4457 Z= 0.371 Chirality : 0.045 0.232 480 Planarity : 0.005 0.051 572 Dihedral : 6.595 27.456 471 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.59 % Allowed : 16.38 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.24 (0.39), residues: 400 helix: -2.04 (1.03), residues: 27 sheet: -0.28 (0.50), residues: 104 loop : -2.06 (0.34), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP H 36 HIS 0.001 0.001 HIS H 35 PHE 0.010 0.002 PHE A 400 TYR 0.020 0.002 TYR L 35 ARG 0.005 0.001 ARG L 44 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 50 time to evaluate : 0.306 Fit side-chains REVERT: A 357 ARG cc_start: 0.7319 (ttt-90) cc_final: 0.7105 (ttt-90) REVERT: A 410 ILE cc_start: 0.8402 (mm) cc_final: 0.8093 (mm) REVERT: A 466 ARG cc_start: 0.8074 (mtm-85) cc_final: 0.7364 (mtm-85) REVERT: A 486 PHE cc_start: 0.6693 (t80) cc_final: 0.6407 (t80) REVERT: A 509 ARG cc_start: 0.7000 (mtt180) cc_final: 0.6074 (mtp180) outliers start: 9 outliers final: 7 residues processed: 59 average time/residue: 0.1685 time to fit residues: 11.9403 Evaluate side-chains 57 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 34 TRP Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.0050 chunk 4 optimal weight: 0.9990 chunk 35 optimal weight: 0.9990 chunk 25 optimal weight: 0.9980 chunk 34 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 2 optimal weight: 0.7980 chunk 27 optimal weight: 0.4980 chunk 13 optimal weight: 0.3980 overall best weight: 0.4994 ------------------------------------------------------------------------------- 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 = 0.4566 r_free = 0.4566 target = 0.191516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.170381 restraints weight = 5172.973| |-----------------------------------------------------------------------------| r_work (start): 0.4348 rms_B_bonded: 2.72 r_work: 0.4255 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.4255 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6130 moved from start: 0.3796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3276 Z= 0.214 Angle : 0.703 8.062 4457 Z= 0.379 Chirality : 0.045 0.217 480 Planarity : 0.005 0.050 572 Dihedral : 6.476 27.138 471 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.72 % Allowed : 17.24 % Favored : 81.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.25 (0.40), residues: 400 helix: -2.04 (1.04), residues: 27 sheet: -0.35 (0.51), residues: 104 loop : -2.03 (0.35), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.002 PHE A 347 TYR 0.018 0.002 TYR L 35 ARG 0.005 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 52 time to evaluate : 0.335 Fit side-chains REVERT: A 357 ARG cc_start: 0.7327 (ttt-90) cc_final: 0.7116 (ttt-90) REVERT: A 410 ILE cc_start: 0.8415 (mm) cc_final: 0.8105 (mm) REVERT: A 465 GLU cc_start: 0.6686 (tp30) cc_final: 0.6365 (tp30) REVERT: A 466 ARG cc_start: 0.7861 (mtm-85) cc_final: 0.7311 (mtm-85) REVERT: A 486 PHE cc_start: 0.6633 (t80) cc_final: 0.6346 (t80) REVERT: A 509 ARG cc_start: 0.7011 (mtt180) cc_final: 0.6101 (mtp180) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.1955 time to fit residues: 13.4058 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 51 time to evaluate : 0.334 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 46 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 22 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 38 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 31 optimal weight: 0.7980 chunk 34 optimal weight: 0.0060 chunk 21 optimal weight: 0.8980 chunk 1 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5394 ------------------------------------------------------------------------------- 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 = 0.4563 r_free = 0.4563 target = 0.191161 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.170153 restraints weight = 5122.111| |-----------------------------------------------------------------------------| r_work (start): 0.4346 rms_B_bonded: 2.72 r_work: 0.4252 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.4252 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.3958 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3276 Z= 0.221 Angle : 0.717 8.035 4457 Z= 0.387 Chirality : 0.045 0.202 480 Planarity : 0.005 0.050 572 Dihedral : 6.466 26.861 471 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 2.01 % Allowed : 17.24 % Favored : 80.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.28 (0.40), residues: 400 helix: -2.02 (1.05), residues: 27 sheet: -0.26 (0.53), residues: 97 loop : -2.08 (0.35), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.011 0.002 PHE A 347 TYR 0.019 0.002 TYR L 35 ARG 0.003 0.001 ARG A 466 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 51 time to evaluate : 0.301 Fit side-chains REVERT: A 357 ARG cc_start: 0.7356 (ttt-90) cc_final: 0.7140 (ttt-90) REVERT: A 410 ILE cc_start: 0.8389 (mm) cc_final: 0.8081 (mm) REVERT: A 465 GLU cc_start: 0.6997 (tp30) cc_final: 0.6786 (tp30) REVERT: A 466 ARG cc_start: 0.7927 (mtm-85) cc_final: 0.7571 (mtm-85) REVERT: A 486 PHE cc_start: 0.6604 (t80) cc_final: 0.6337 (t80) REVERT: A 509 ARG cc_start: 0.6964 (mtt180) cc_final: 0.6062 (mtp180) REVERT: H 103 ASP cc_start: 0.7665 (t0) cc_final: 0.7377 (m-30) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.1716 time to fit residues: 11.9496 Evaluate side-chains 56 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain A residue 438 SER Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 74 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 24 optimal weight: 0.9990 chunk 21 optimal weight: 0.9980 chunk 32 optimal weight: 0.9990 chunk 25 optimal weight: 0.6980 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.0970 chunk 23 optimal weight: 0.4980 chunk 3 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 overall best weight: 0.4978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 91 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4568 r_free = 0.4568 target = 0.191484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4361 r_free = 0.4361 target = 0.170001 restraints weight = 5099.896| |-----------------------------------------------------------------------------| r_work (start): 0.4345 rms_B_bonded: 2.82 r_work: 0.4248 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4248 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6136 moved from start: 0.4086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3276 Z= 0.214 Angle : 0.709 7.855 4457 Z= 0.383 Chirality : 0.045 0.179 480 Planarity : 0.005 0.049 572 Dihedral : 6.336 25.026 471 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.44 % Allowed : 18.10 % Favored : 80.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.29 (0.40), residues: 400 helix: -2.12 (0.90), residues: 33 sheet: -0.58 (0.50), residues: 110 loop : -1.96 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.002 PHE A 347 TYR 0.018 0.002 TYR L 35 ARG 0.002 0.000 ARG H 97 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 800 Ramachandran restraints generated. 400 Oldfield, 0 Emsley, 400 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.381 Fit side-chains REVERT: A 357 ARG cc_start: 0.7400 (ttt-90) cc_final: 0.7155 (ttt-90) REVERT: A 410 ILE cc_start: 0.8423 (mm) cc_final: 0.8144 (mm) REVERT: A 466 ARG cc_start: 0.7945 (mtm-85) cc_final: 0.7682 (mtm-85) REVERT: A 486 PHE cc_start: 0.6596 (t80) cc_final: 0.6354 (t80) REVERT: H 103 ASP cc_start: 0.7664 (t0) cc_final: 0.7387 (m-30) outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.1723 time to fit residues: 11.5646 Evaluate side-chains 55 residues out of total 348 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 400 PHE Chi-restraints excluded: chain A residue 402 ILE Chi-restraints excluded: chain H residue 7 SER Chi-restraints excluded: chain L residue 46 LEU Chi-restraints excluded: chain L residue 75 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 39 random chunks: chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 38 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 8 optimal weight: 0.8980 chunk 23 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- 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 = 0.4554 r_free = 0.4554 target = 0.190321 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.168935 restraints weight = 5179.306| |-----------------------------------------------------------------------------| r_work (start): 0.4332 rms_B_bonded: 2.84 r_work: 0.4235 rms_B_bonded: 3.26 restraints_weight: 0.5000 r_work (final): 0.4235 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6166 moved from start: 0.4232 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3276 Z= 0.242 Angle : 0.739 7.722 4457 Z= 0.399 Chirality : 0.045 0.173 480 Planarity : 0.005 0.050 572 Dihedral : 6.467 24.777 471 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.75 % Favored : 94.25 % Rotamer: Outliers : 1.15 % Allowed : 18.97 % Favored : 79.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: -2.40 (0.40), residues: 400 helix: -2.25 (0.88), residues: 33 sheet: -0.44 (0.53), residues: 101 loop : -2.11 (0.35), residues: 266 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.003 TRP H 36 HIS 0.002 0.001 HIS H 35 PHE 0.012 0.002 PHE A 497 TYR 0.020 0.002 TYR L 35 ARG 0.003 0.001 ARG H 97 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2030.85 seconds wall clock time: 35 minutes 53.17 seconds (2153.17 seconds total)