Starting phenix.real_space_refine on Wed Mar 5 21:02:04 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7yr0_34041/03_2025/7yr0_34041.cif Found real_map, /net/cci-nas-00/data/ceres_data/7yr0_34041/03_2025/7yr0_34041.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.98 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7yr0_34041/03_2025/7yr0_34041.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7yr0_34041/03_2025/7yr0_34041.map" model { file = "/net/cci-nas-00/data/ceres_data/7yr0_34041/03_2025/7yr0_34041.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7yr0_34041/03_2025/7yr0_34041.cif" } resolution = 3.98 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= 0.044 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2149 2.51 5 N 571 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 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: 3383 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1560 Classifications: {'peptide': 196} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 12, 'TRANS': 183} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "C" Number of atoms: 959 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 959 Classifications: {'peptide': 123} Link IDs: {'PTRANS': 3, 'TRANS': 119} Chain: "B" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 815 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain: "D" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {'BMA': 1, 'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 12 Unresolved non-hydrogen chiralities: 4 Time building chain proxies: 3.40, per 1000 atoms: 1.01 Number of scatterers: 3383 At special positions: 0 Unit cell: (73.83, 85.6, 81.32, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 648 8.00 N 571 7.00 C 2149 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 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied BETA1-4 " NAG D 1 " - " NAG D 2 " " NAG D 2 " - " BMA D 3 " BETA1-6 " NAG D 1 " - " FUC D 4 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG D 1 " - " ASN A 343 " Time building additional restraints: 0.97 Conformation dependent library (CDL) restraints added in 405.5 milliseconds 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 774 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 8 sheets defined 6.3% alpha, 24.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 337 through 342 removed outlier: 3.995A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N PHE A 342 " --> pdb=" O PHE A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.799A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 387 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'C' and resid 61 through 65 Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 358 removed outlier: 4.310A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 3.812A pdb=" N SER A 399 " --> pdb=" O ASN A 354 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.597A pdb=" N TYR A 453 " --> pdb=" O GLN A 493 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 3 through 6 Processing sheet with id=AA4, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.890A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) removed outlier: 4.440A pdb=" N ASN C 116 " --> pdb=" O ARG C 98 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 49 through 51 removed outlier: 3.890A pdb=" N GLY C 33 " --> pdb=" O ASP C 99 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.697A pdb=" N LEU B 11 " --> pdb=" O LYS B 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'B' and resid 19 through 22 removed outlier: 3.763A pdb=" N ASP B 71 " --> pdb=" O SER B 68 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 46 through 47 removed outlier: 4.117A pdb=" N THR B 97 " --> pdb=" O GLN B 91 " (cutoff:3.500A) 82 hydrogen bonds defined for protein. 189 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: 0.78 Time building geometry restraints manager: 1.13 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 1073 1.35 - 1.46: 942 1.46 - 1.58: 1439 1.58 - 1.70: 0 1.70 - 1.82: 18 Bond restraints: 3472 Sorted by residual: bond pdb=" C1 BMA D 3 " pdb=" C2 BMA D 3 " ideal model delta sigma weight residual 1.519 1.547 -0.028 2.00e-02 2.50e+03 1.96e+00 bond pdb=" C2 NAG D 2 " pdb=" N2 NAG D 2 " ideal model delta sigma weight residual 1.439 1.464 -0.025 2.00e-02 2.50e+03 1.58e+00 bond pdb=" CA GLY A 381 " pdb=" C GLY A 381 " ideal model delta sigma weight residual 1.512 1.523 -0.011 8.70e-03 1.32e+04 1.56e+00 bond pdb=" C5 NAG D 1 " pdb=" O5 NAG D 1 " ideal model delta sigma weight residual 1.413 1.437 -0.024 2.00e-02 2.50e+03 1.38e+00 bond pdb=" C5 NAG D 2 " pdb=" O5 NAG D 2 " ideal model delta sigma weight residual 1.413 1.436 -0.023 2.00e-02 2.50e+03 1.36e+00 ... (remaining 3467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.26: 4462 1.26 - 2.51: 185 2.51 - 3.77: 51 3.77 - 5.02: 17 5.02 - 6.28: 5 Bond angle restraints: 4720 Sorted by residual: angle pdb=" N ILE A 402 " pdb=" CA ILE A 402 " pdb=" C ILE A 402 " ideal model delta sigma weight residual 108.53 111.81 -3.28 1.22e+00 6.72e-01 7.23e+00 angle pdb=" C GLU C 82 " pdb=" CA GLU C 82 " pdb=" CB GLU C 82 " ideal model delta sigma weight residual 110.42 115.40 -4.98 1.99e+00 2.53e-01 6.25e+00 angle pdb=" C GLU B 80 " pdb=" CA GLU B 80 " pdb=" CB GLU B 80 " ideal model delta sigma weight residual 109.26 112.83 -3.57 1.47e+00 4.63e-01 5.91e+00 angle pdb=" C MET C 48 " pdb=" N GLY C 49 " pdb=" CA GLY C 49 " ideal model delta sigma weight residual 121.46 119.21 2.25 9.50e-01 1.11e+00 5.63e+00 angle pdb=" N GLY C 49 " pdb=" CA GLY C 49 " pdb=" C GLY C 49 " ideal model delta sigma weight residual 110.90 114.36 -3.46 1.53e+00 4.27e-01 5.12e+00 ... (remaining 4715 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.07: 1915 22.07 - 44.14: 136 44.14 - 66.21: 11 66.21 - 88.28: 9 88.28 - 110.35: 5 Dihedral angle restraints: 2076 sinusoidal: 851 harmonic: 1225 Sorted by residual: dihedral pdb=" CA SER B 7 " pdb=" C SER B 7 " pdb=" N PRO B 8 " pdb=" CA PRO B 8 " ideal model delta harmonic sigma weight residual 180.00 154.07 25.93 0 5.00e+00 4.00e-02 2.69e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 54.67 38.33 1 1.00e+01 1.00e-02 2.07e+01 dihedral pdb=" CA TYR C 80 " pdb=" C TYR C 80 " pdb=" N MET C 81 " pdb=" CA MET C 81 " ideal model delta harmonic sigma weight residual 180.00 157.93 22.07 0 5.00e+00 4.00e-02 1.95e+01 ... (remaining 2073 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 448 0.066 - 0.133: 61 0.133 - 0.199: 4 0.199 - 0.265: 0 0.265 - 0.331: 2 Chirality restraints: 515 Sorted by residual: chirality pdb=" C1 NAG D 1 " pdb=" ND2 ASN A 343 " pdb=" C2 NAG D 1 " pdb=" O5 NAG D 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.07 -0.33 2.00e-01 2.50e+01 2.74e+00 chirality pdb=" C5 BMA D 3 " pdb=" C4 BMA D 3 " pdb=" C6 BMA D 3 " pdb=" O5 BMA D 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.83e+00 chirality pdb=" C2 NAG D 2 " pdb=" C1 NAG D 2 " pdb=" C3 NAG D 2 " pdb=" N2 NAG D 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.31 -0.19 2.00e-01 2.50e+01 8.59e-01 ... (remaining 512 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 7 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.86e+00 pdb=" N PRO B 8 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 8 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 8 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP C 47 " 0.006 2.00e-02 2.50e+03 1.16e-02 1.35e+00 pdb=" C TRP C 47 " -0.020 2.00e-02 2.50e+03 pdb=" O TRP C 47 " 0.008 2.00e-02 2.50e+03 pdb=" N MET C 48 " 0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP C 47 " 0.009 2.00e-02 2.50e+03 7.14e-03 1.27e+00 pdb=" CG TRP C 47 " -0.020 2.00e-02 2.50e+03 pdb=" CD1 TRP C 47 " 0.007 2.00e-02 2.50e+03 pdb=" CD2 TRP C 47 " 0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP C 47 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP C 47 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP C 47 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP C 47 " 0.000 2.00e-02 2.50e+03 pdb=" CZ3 TRP C 47 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP C 47 " 0.001 2.00e-02 2.50e+03 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 130 2.71 - 3.26: 3238 3.26 - 3.81: 5061 3.81 - 4.35: 6100 4.35 - 4.90: 10380 Nonbonded interactions: 24909 Sorted by model distance: nonbonded pdb=" OG1 THR C 69 " pdb=" OE2 GLU C 82 " model vdw 2.164 3.040 nonbonded pdb=" O VAL B 3 " pdb=" OG SER B 26 " model vdw 2.229 3.040 nonbonded pdb=" OG SER C 35 " pdb=" OD2 ASP C 99 " model vdw 2.250 3.040 nonbonded pdb=" NH1 ARG C 87 " pdb=" OD1 ASP C 89 " model vdw 2.253 3.120 nonbonded pdb=" O ALA A 419 " pdb=" NZ LYS A 424 " model vdw 2.259 3.120 ... (remaining 24904 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.620 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: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.850 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7653 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 0.028 3472 Z= 0.204 Angle : 0.681 6.280 4720 Z= 0.347 Chirality : 0.049 0.331 515 Planarity : 0.004 0.034 605 Dihedral : 15.968 110.350 1287 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 11.64 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.31 % Favored : 91.45 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.76 (0.43), residues: 421 helix: -0.21 (3.10), residues: 6 sheet: 0.50 (0.59), residues: 92 loop : -1.86 (0.35), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 47 HIS 0.002 0.001 HIS B 92 PHE 0.017 0.001 PHE C 29 TYR 0.012 0.001 TYR B 50 ARG 0.003 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.353 Fit side-chains REVERT: C 80 TYR cc_start: 0.8049 (m-80) cc_final: 0.7822 (m-80) outliers start: 0 outliers final: 0 residues processed: 75 average time/residue: 0.1754 time to fit residues: 15.8285 Evaluate side-chains 57 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 5.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 0.4980 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.3706 r_free = 0.3706 target = 0.121880 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3286 r_free = 0.3286 target = 0.095506 restraints weight = 8020.876| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.097856 restraints weight = 5535.069| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3354 r_free = 0.3354 target = 0.099512 restraints weight = 4356.354| |-----------------------------------------------------------------------------| r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 3472 Z= 0.312 Angle : 0.702 9.632 4720 Z= 0.348 Chirality : 0.048 0.235 515 Planarity : 0.004 0.037 605 Dihedral : 10.015 63.953 552 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.67 Ramachandran Plot: Outliers : 0.48 % Allowed : 9.98 % Favored : 89.55 % Rotamer: Outliers : 1.40 % Allowed : 13.76 % Favored : 84.83 % 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: -1.95 (0.42), residues: 421 helix: -2.60 (1.22), residues: 18 sheet: 0.24 (0.58), residues: 98 loop : -1.89 (0.36), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.004 0.002 HIS B 92 PHE 0.012 0.002 PHE C 29 TYR 0.026 0.002 TYR B 50 ARG 0.010 0.001 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 63 time to evaluate : 0.935 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8082 (m110) cc_final: 0.7825 (p0) outliers start: 5 outliers final: 4 residues processed: 66 average time/residue: 0.1747 time to fit residues: 14.0578 Evaluate side-chains 62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 12 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 35 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 3 optimal weight: 0.0010 chunk 23 optimal weight: 0.0370 overall best weight: 0.4464 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3744 r_free = 0.3744 target = 0.124824 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3330 r_free = 0.3330 target = 0.098244 restraints weight = 7859.228| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.100881 restraints weight = 5189.919| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.102731 restraints weight = 3991.612| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3472 Z= 0.172 Angle : 0.653 9.577 4720 Z= 0.312 Chirality : 0.046 0.279 515 Planarity : 0.004 0.035 605 Dihedral : 7.631 59.245 552 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.13 % Favored : 92.64 % Rotamer: Outliers : 1.97 % Allowed : 15.17 % Favored : 82.87 % 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: -1.87 (0.41), residues: 421 helix: -1.91 (1.27), residues: 20 sheet: 0.57 (0.59), residues: 92 loop : -1.94 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.002 0.001 HIS B 92 PHE 0.019 0.001 PHE C 29 TYR 0.023 0.001 TYR B 50 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.385 Fit side-chains revert: symmetry clash REVERT: A 405 ASN cc_start: 0.8032 (m110) cc_final: 0.7802 (p0) REVERT: C 80 TYR cc_start: 0.8101 (m-80) cc_final: 0.7860 (m-80) REVERT: C 82 GLU cc_start: 0.5878 (pp20) cc_final: 0.5467 (tm-30) outliers start: 7 outliers final: 4 residues processed: 73 average time/residue: 0.1804 time to fit residues: 15.9015 Evaluate side-chains 62 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.570 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 7 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 12 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 24 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.3738 r_free = 0.3738 target = 0.124857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.100278 restraints weight = 7860.254| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.102749 restraints weight = 5311.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 23)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104365 restraints weight = 4115.366| |-----------------------------------------------------------------------------| r_work (final): 0.3405 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7724 moved from start: 0.1709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3472 Z= 0.199 Angle : 0.636 9.535 4720 Z= 0.310 Chirality : 0.046 0.260 515 Planarity : 0.003 0.036 605 Dihedral : 7.055 59.054 552 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 9.52 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.79 % Favored : 90.97 % Rotamer: Outliers : 2.25 % Allowed : 17.98 % Favored : 79.78 % 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: -1.81 (0.41), residues: 421 helix: -1.76 (1.36), residues: 20 sheet: 0.71 (0.60), residues: 90 loop : -1.93 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS A 339 PHE 0.015 0.001 PHE C 29 TYR 0.017 0.001 TYR A 501 ARG 0.002 0.000 ARG A 509 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 64 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: C 80 TYR cc_start: 0.8066 (m-80) cc_final: 0.7816 (m-80) REVERT: C 82 GLU cc_start: 0.5830 (pp20) cc_final: 0.5353 (tm-30) outliers start: 8 outliers final: 5 residues processed: 69 average time/residue: 0.1689 time to fit residues: 14.1156 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 59 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.9990 chunk 34 optimal weight: 7.9990 chunk 23 optimal weight: 0.0970 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.0670 chunk 16 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 18 optimal weight: 0.7980 chunk 12 optimal weight: 2.9990 overall best weight: 0.5516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.125585 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3372 r_free = 0.3372 target = 0.101035 restraints weight = 7825.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3412 r_free = 0.3412 target = 0.103545 restraints weight = 5284.476| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.105191 restraints weight = 4082.480| |-----------------------------------------------------------------------------| r_work (final): 0.3420 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7700 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3472 Z= 0.182 Angle : 0.643 9.566 4720 Z= 0.312 Chirality : 0.046 0.270 515 Planarity : 0.003 0.033 605 Dihedral : 6.789 58.060 552 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 9.37 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.36 % Favored : 92.40 % Rotamer: Outliers : 2.53 % Allowed : 21.07 % Favored : 76.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.42), residues: 421 helix: -1.94 (1.78), residues: 12 sheet: 0.64 (0.59), residues: 92 loop : -1.76 (0.35), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.015 0.003 HIS A 505 PHE 0.008 0.001 PHE A 374 TYR 0.015 0.001 TYR C 27 ARG 0.001 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 62 time to evaluate : 0.346 Fit side-chains revert: symmetry clash REVERT: C 82 GLU cc_start: 0.5731 (pp20) cc_final: 0.5399 (tm-30) outliers start: 9 outliers final: 7 residues processed: 67 average time/residue: 0.1658 time to fit residues: 13.5008 Evaluate side-chains 64 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 57 time to evaluate : 0.383 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 33 optimal weight: 0.0770 chunk 0 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 40 optimal weight: 2.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.2142 ------------------------------------------------------------------------------- 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 = 0.3710 r_free = 0.3710 target = 0.122839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.097685 restraints weight = 8095.095| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.100093 restraints weight = 5410.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3386 r_free = 0.3386 target = 0.101861 restraints weight = 4198.691| |-----------------------------------------------------------------------------| r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.2084 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3472 Z= 0.264 Angle : 0.668 9.546 4720 Z= 0.331 Chirality : 0.047 0.251 515 Planarity : 0.004 0.035 605 Dihedral : 6.845 58.528 552 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 9.82 Ramachandran Plot: Outliers : 0.24 % Allowed : 9.98 % Favored : 89.79 % Rotamer: Outliers : 2.53 % Allowed : 20.51 % Favored : 76.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.41), residues: 421 helix: -2.03 (1.28), residues: 20 sheet: 0.64 (0.59), residues: 90 loop : -1.93 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.003 0.001 HIS A 339 PHE 0.008 0.001 PHE B 98 TYR 0.017 0.002 TYR C 27 ARG 0.003 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 61 time to evaluate : 0.348 Fit side-chains revert: symmetry clash REVERT: C 82 GLU cc_start: 0.5928 (pp20) cc_final: 0.5498 (tm-30) REVERT: B 27 GLN cc_start: 0.7262 (OUTLIER) cc_final: 0.6869 (pp30) outliers start: 9 outliers final: 5 residues processed: 66 average time/residue: 0.1814 time to fit residues: 14.4983 Evaluate side-chains 60 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 54 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain B residue 11 LEU Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 82 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 2 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 5 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 13 optimal weight: 0.0070 chunk 10 optimal weight: 0.6980 chunk 22 optimal weight: 6.9990 chunk 8 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 7 optimal weight: 4.9990 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3742 r_free = 0.3742 target = 0.124916 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.099919 restraints weight = 7907.983| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.102459 restraints weight = 5238.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.104224 restraints weight = 4025.762| |-----------------------------------------------------------------------------| r_work (final): 0.3408 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3472 Z= 0.180 Angle : 0.653 9.495 4720 Z= 0.322 Chirality : 0.048 0.271 515 Planarity : 0.003 0.033 605 Dihedral : 6.559 57.493 552 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.36 % Favored : 92.40 % Rotamer: Outliers : 4.49 % Allowed : 18.82 % Favored : 76.69 % 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: -1.83 (0.41), residues: 421 helix: -2.05 (1.27), residues: 20 sheet: 0.53 (0.58), residues: 95 loop : -1.90 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 436 HIS 0.019 0.004 HIS A 505 PHE 0.008 0.001 PHE A 377 TYR 0.017 0.001 TYR C 27 ARG 0.004 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 62 time to evaluate : 0.383 Fit side-chains revert: symmetry clash REVERT: A 434 ILE cc_start: 0.9271 (OUTLIER) cc_final: 0.8962 (mt) REVERT: C 82 GLU cc_start: 0.5864 (OUTLIER) cc_final: 0.5508 (tm-30) outliers start: 16 outliers final: 7 residues processed: 70 average time/residue: 0.1700 time to fit residues: 14.3706 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 10 optimal weight: 0.9990 chunk 28 optimal weight: 3.9990 chunk 30 optimal weight: 0.0170 chunk 20 optimal weight: 0.0010 chunk 1 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 22 optimal weight: 6.9990 chunk 34 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 5 optimal weight: 0.7980 overall best weight: 0.4624 ------------------------------------------------------------------------------- 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 = 0.3747 r_free = 0.3747 target = 0.125179 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3363 r_free = 0.3363 target = 0.100494 restraints weight = 7890.994| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.102966 restraints weight = 5304.358| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3430 r_free = 0.3430 target = 0.104706 restraints weight = 4096.607| |-----------------------------------------------------------------------------| r_work (final): 0.3417 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3472 Z= 0.173 Angle : 0.648 9.570 4720 Z= 0.320 Chirality : 0.046 0.256 515 Planarity : 0.003 0.035 605 Dihedral : 6.360 58.259 552 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 8.31 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.84 % Favored : 91.92 % Rotamer: Outliers : 3.93 % Allowed : 18.54 % Favored : 77.53 % 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: -1.86 (0.41), residues: 421 helix: -2.23 (1.20), residues: 20 sheet: 0.56 (0.58), residues: 95 loop : -1.92 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 47 HIS 0.001 0.001 HIS A 339 PHE 0.005 0.001 PHE A 400 TYR 0.017 0.001 TYR C 27 ARG 0.001 0.000 ARG C 87 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 60 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 490 PHE cc_start: 0.6209 (OUTLIER) cc_final: 0.5823 (t80) REVERT: C 82 GLU cc_start: 0.5841 (OUTLIER) cc_final: 0.5492 (tm-30) outliers start: 14 outliers final: 8 residues processed: 66 average time/residue: 0.1890 time to fit residues: 15.5631 Evaluate side-chains 68 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 58 time to evaluate : 0.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 0 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 11 optimal weight: 0.0370 chunk 14 optimal weight: 0.0980 chunk 19 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 6 optimal weight: 3.9990 chunk 22 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 overall best weight: 0.5462 ------------------------------------------------------------------------------- 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 = 0.3748 r_free = 0.3748 target = 0.125384 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.100084 restraints weight = 7865.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.102634 restraints weight = 5278.740| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.104378 restraints weight = 4044.625| |-----------------------------------------------------------------------------| r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.2292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3472 Z= 0.182 Angle : 0.654 9.602 4720 Z= 0.320 Chirality : 0.045 0.247 515 Planarity : 0.003 0.032 605 Dihedral : 6.305 58.446 552 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 8.01 Ramachandran Plot: Outliers : 0.24 % Allowed : 7.84 % Favored : 91.92 % Rotamer: Outliers : 3.65 % Allowed : 18.26 % Favored : 78.09 % 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: -1.85 (0.41), residues: 421 helix: -2.29 (1.19), residues: 20 sheet: 0.58 (0.59), residues: 95 loop : -1.91 (0.35), residues: 306 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 47 HIS 0.002 0.001 HIS A 339 PHE 0.006 0.001 PHE A 400 TYR 0.016 0.001 TYR C 27 ARG 0.002 0.000 ARG B 78 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 60 time to evaluate : 0.482 Fit side-chains revert: symmetry clash REVERT: A 490 PHE cc_start: 0.6257 (OUTLIER) cc_final: 0.5860 (t80) REVERT: C 82 GLU cc_start: 0.5869 (OUTLIER) cc_final: 0.5504 (tm-30) outliers start: 13 outliers final: 10 residues processed: 66 average time/residue: 0.1788 time to fit residues: 14.4509 Evaluate side-chains 69 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 57 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain A residue 508 TYR Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 17 optimal weight: 0.9990 chunk 35 optimal weight: 0.6980 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 0.2980 chunk 39 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 29 optimal weight: 0.5980 chunk 36 optimal weight: 5.9990 chunk 30 optimal weight: 0.8980 chunk 34 optimal weight: 5.9990 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 = 0.3745 r_free = 0.3745 target = 0.125217 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.099809 restraints weight = 7868.782| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.102265 restraints weight = 5249.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.104113 restraints weight = 4050.261| |-----------------------------------------------------------------------------| r_work (final): 0.3398 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3472 Z= 0.199 Angle : 0.670 9.621 4720 Z= 0.330 Chirality : 0.046 0.244 515 Planarity : 0.003 0.035 605 Dihedral : 6.363 58.917 552 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.24 % Allowed : 8.08 % Favored : 91.69 % Rotamer: Outliers : 3.37 % Allowed : 19.38 % Favored : 77.25 % 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: -1.82 (0.41), residues: 421 helix: -2.37 (1.16), residues: 20 sheet: 0.60 (0.59), residues: 93 loop : -1.87 (0.35), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 47 HIS 0.002 0.001 HIS A 339 PHE 0.007 0.001 PHE A 400 TYR 0.017 0.001 TYR C 27 ARG 0.002 0.000 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 842 Ramachandran restraints generated. 421 Oldfield, 0 Emsley, 421 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 59 time to evaluate : 0.355 Fit side-chains revert: symmetry clash REVERT: A 490 PHE cc_start: 0.6233 (OUTLIER) cc_final: 0.5820 (t80) REVERT: C 82 GLU cc_start: 0.5891 (OUTLIER) cc_final: 0.5539 (tm-30) outliers start: 12 outliers final: 9 residues processed: 65 average time/residue: 0.1646 time to fit residues: 13.0220 Evaluate side-chains 67 residues out of total 358 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 56 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 374 PHE Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 490 PHE Chi-restraints excluded: chain C residue 82 GLU Chi-restraints excluded: chain B residue 28 THR Chi-restraints excluded: chain B residue 82 GLU Chi-restraints excluded: chain B residue 106 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 7.9990 chunk 18 optimal weight: 2.9990 chunk 20 optimal weight: 0.0970 chunk 10 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 0 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.8184 ------------------------------------------------------------------------------- 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 = 0.3695 r_free = 0.3695 target = 0.121741 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.095864 restraints weight = 8045.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.098181 restraints weight = 5435.689| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3350 r_free = 0.3350 target = 0.099901 restraints weight = 4266.892| |-----------------------------------------------------------------------------| r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7848 moved from start: 0.2580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.054 3472 Z= 0.355 Angle : 0.743 9.658 4720 Z= 0.371 Chirality : 0.047 0.234 515 Planarity : 0.004 0.033 605 Dihedral : 7.022 59.819 552 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 11.49 Ramachandran Plot: Outliers : 0.48 % Allowed : 10.93 % Favored : 88.60 % Rotamer: Outliers : 3.09 % Allowed : 19.66 % Favored : 77.25 % 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: -1.97 (0.41), residues: 421 helix: -2.44 (1.16), residues: 20 sheet: 0.38 (0.58), residues: 90 loop : -1.92 (0.34), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 47 HIS 0.004 0.001 HIS A 339 PHE 0.018 0.002 PHE A 429 TYR 0.017 0.002 TYR C 27 ARG 0.003 0.000 ARG C 87 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1534.74 seconds wall clock time: 27 minutes 19.48 seconds (1639.48 seconds total)