Starting phenix.real_space_refine on Tue Feb 13 09:51:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv5_35741/02_2024/8iv5_35741.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv5_35741/02_2024/8iv5_35741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.77 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv5_35741/02_2024/8iv5_35741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv5_35741/02_2024/8iv5_35741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv5_35741/02_2024/8iv5_35741.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iv5_35741/02_2024/8iv5_35741.pdb" } resolution = 3.77 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 29 5.16 5 C 3221 2.51 5 N 857 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "G ARG 357": "NH1" <-> "NH2" Residue "G ASP 405": "OD1" <-> "OD2" Residue "G ARG 408": "NH1" <-> "NH2" Residue "G ASP 420": "OD1" <-> "OD2" Residue "G ASP 427": "OD1" <-> "OD2" Residue "G TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L ASP 60": "OD1" <-> "OD2" Residue "H GLU 1": "OE1" <-> "OE2" Residue "H ASP 107": "OD1" <-> "OD2" Residue "B ASP 1": "OD1" <-> "OD2" Residue "B ASP 82": "OD1" <-> "OD2" Residue "A TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 105": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5096 Number of models: 1 Model: "" Number of chains: 6 Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "L" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 836 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 102} Chain: "H" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 921 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 2, 'TRANS': 115} Chain: "B" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 817 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 101} Chain: "A" Number of atoms: 947 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 947 Classifications: {'peptide': 119} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 114} Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.46, per 1000 atoms: 0.68 Number of scatterers: 5096 At special positions: 0 Unit cell: (113.588, 73.132, 79.356, 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 29 16.00 O 989 8.00 N 857 7.00 C 3221 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 98 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 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 C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG C 1 " - " ASN G 343 " Time building additional restraints: 2.00 Conformation dependent library (CDL) restraints added in 957.1 milliseconds 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 14 sheets defined 6.5% alpha, 24.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.61 Creating SS restraints... Processing helix chain 'G' and resid 337 through 343 removed outlier: 3.832A pdb=" N VAL G 341 " --> pdb=" O PRO G 337 " (cutoff:3.500A) removed outlier: 3.596A pdb=" N PHE G 342 " --> pdb=" O PHE G 338 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN G 343 " --> pdb=" O GLY G 339 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 337 through 343' Processing helix chain 'G' and resid 365 through 370 Processing helix chain 'G' and resid 403 through 407 removed outlier: 3.516A pdb=" N GLU G 406 " --> pdb=" O ARG G 403 " (cutoff:3.500A) Processing helix chain 'G' and resid 502 through 506 removed outlier: 3.520A pdb=" N GLN G 506 " --> pdb=" O VAL G 503 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 57 Processing helix chain 'B' and resid 79 through 83 removed outlier: 3.599A pdb=" N ASP B 82 " --> pdb=" O GLU B 79 " (cutoff:3.500A) removed outlier: 3.629A pdb=" N PHE B 83 " --> pdb=" O THR B 80 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 79 through 83' Processing helix chain 'A' and resid 28 through 32 removed outlier: 4.028A pdb=" N TYR A 32 " --> pdb=" O PHE A 29 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.812A pdb=" N ARG A 65 " --> pdb=" O ASP A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.857A pdb=" N ASN G 354 " --> pdb=" O SER G 399 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N SER G 399 " --> pdb=" O ASN G 354 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AA4, first strand: chain 'L' and resid 10 through 11 Processing sheet with id=AA5, first strand: chain 'L' and resid 18 through 23 removed outlier: 3.999A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 53 through 54 removed outlier: 3.666A pdb=" N TYR L 49 " --> pdb=" O ASN L 53 " (cutoff:3.500A) removed outlier: 6.533A pdb=" N TRP L 35 " --> pdb=" O MET L 47 " (cutoff:3.500A) removed outlier: 5.117A pdb=" N TYR L 49 " --> pdb=" O VAL L 33 " (cutoff:3.500A) removed outlier: 7.013A pdb=" N VAL L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.614A pdb=" N VAL H 12 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET H 34 " --> pdb=" O GLN H 50 " (cutoff:3.500A) removed outlier: 5.026A pdb=" N GLN H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.834A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 17 through 23 removed outlier: 3.519A pdb=" N MET H 85 " --> pdb=" O MET H 18 " (cutoff:3.500A) removed outlier: 3.853A pdb=" N SER H 80 " --> pdb=" O ASP H 75 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP H 75 " --> pdb=" O SER H 80 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'B' and resid 19 through 20 removed outlier: 3.613A pdb=" N VAL B 19 " --> pdb=" O ILE B 75 " (cutoff:3.500A) removed outlier: 3.925A pdb=" N THR B 72 " --> pdb=" O SER B 65 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 45 through 48 removed outlier: 6.905A pdb=" N TRP B 35 " --> pdb=" O LEU B 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 3 through 6 removed outlier: 3.963A pdb=" N GLN A 3 " --> pdb=" O SER A 25 " (cutoff:3.500A) removed outlier: 3.895A pdb=" N SER A 25 " --> pdb=" O GLN A 3 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 10 through 12 removed outlier: 6.727A pdb=" N GLU A 10 " --> pdb=" O THR A 116 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N VAL A 37 " --> pdb=" O PHE A 95 " (cutoff:3.500A) removed outlier: 6.664A pdb=" N LEU A 34 " --> pdb=" O TRP A 50 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N TRP A 50 " --> pdb=" O LEU A 34 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP A 36 " --> pdb=" O MET A 48 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 18 through 20 removed outlier: 3.617A pdb=" N VAL A 18 " --> pdb=" O ILE A 83 " (cutoff:3.500A) 113 hydrogen bonds defined for protein. 264 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.30 Time building geometry restraints manager: 2.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1619 1.34 - 1.46: 1311 1.46 - 1.58: 2252 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 5221 Sorted by residual: bond pdb=" C GLN G 506 " pdb=" N PRO G 507 " ideal model delta sigma weight residual 1.333 1.356 -0.022 1.01e-02 9.80e+03 4.88e+00 bond pdb=" C5 BMA C 3 " pdb=" O5 BMA C 3 " ideal model delta sigma weight residual 1.417 1.451 -0.034 2.00e-02 2.50e+03 2.95e+00 bond pdb=" N ASN B 31 " pdb=" CA ASN B 31 " ideal model delta sigma weight residual 1.457 1.477 -0.019 1.29e-02 6.01e+03 2.25e+00 bond pdb=" CB TRP H 47 " pdb=" CG TRP H 47 " ideal model delta sigma weight residual 1.498 1.453 0.045 3.10e-02 1.04e+03 2.07e+00 bond pdb=" CA VAL H 48 " pdb=" CB VAL H 48 " ideal model delta sigma weight residual 1.545 1.532 0.013 9.10e-03 1.21e+04 1.94e+00 ... (remaining 5216 not shown) Histogram of bond angle deviations from ideal: 99.95 - 106.78: 142 106.78 - 113.61: 2764 113.61 - 120.44: 1977 120.44 - 127.27: 2141 127.27 - 134.11: 58 Bond angle restraints: 7082 Sorted by residual: angle pdb=" C SER B 40 " pdb=" N HIS B 41 " pdb=" CA HIS B 41 " ideal model delta sigma weight residual 122.82 128.23 -5.41 1.42e+00 4.96e-01 1.45e+01 angle pdb=" N GLY G 404 " pdb=" CA GLY G 404 " pdb=" C GLY G 404 " ideal model delta sigma weight residual 112.49 116.54 -4.05 1.21e+00 6.83e-01 1.12e+01 angle pdb=" C SER L 76 " pdb=" N ASN L 77 " pdb=" CA ASN L 77 " ideal model delta sigma weight residual 122.82 127.52 -4.70 1.42e+00 4.96e-01 1.10e+01 angle pdb=" C SER B 30 " pdb=" N ASN B 31 " pdb=" CA ASN B 31 " ideal model delta sigma weight residual 121.54 127.54 -6.00 1.91e+00 2.74e-01 9.86e+00 angle pdb=" C GLY A 66 " pdb=" N ARG A 67 " pdb=" CA ARG A 67 " ideal model delta sigma weight residual 121.54 127.44 -5.90 1.91e+00 2.74e-01 9.56e+00 ... (remaining 7077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.02: 2822 20.02 - 40.03: 237 40.03 - 60.05: 28 60.05 - 80.07: 11 80.07 - 100.08: 4 Dihedral angle restraints: 3102 sinusoidal: 1251 harmonic: 1851 Sorted by residual: dihedral pdb=" CB CYS G 480 " pdb=" SG CYS G 480 " pdb=" SG CYS G 488 " pdb=" CB CYS G 488 " ideal model delta sinusoidal sigma weight residual -86.00 -133.64 47.64 1 1.00e+01 1.00e-02 3.13e+01 dihedral pdb=" CA CYS G 480 " pdb=" C CYS G 480 " pdb=" N ASN G 481 " pdb=" CA ASN G 481 " ideal model delta harmonic sigma weight residual 180.00 154.30 25.70 0 5.00e+00 4.00e-02 2.64e+01 dihedral pdb=" CA TYR A 60 " pdb=" C TYR A 60 " pdb=" N ASN A 61 " pdb=" CA ASN A 61 " ideal model delta harmonic sigma weight residual 180.00 155.27 24.73 0 5.00e+00 4.00e-02 2.45e+01 ... (remaining 3099 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.057: 563 0.057 - 0.113: 155 0.113 - 0.170: 39 0.170 - 0.227: 6 0.227 - 0.284: 1 Chirality restraints: 764 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.56 0.28 2.00e-01 2.50e+01 2.01e+00 chirality pdb=" CA TYR L 94 " pdb=" N TYR L 94 " pdb=" C TYR L 94 " pdb=" CB TYR L 94 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE A 51 " pdb=" CA ILE A 51 " pdb=" CG1 ILE A 51 " pdb=" CG2 ILE A 51 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 ... (remaining 761 not shown) Planarity restraints: 911 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR L 94 " -0.044 5.00e-02 4.00e+02 6.61e-02 7.00e+00 pdb=" N PRO L 95 " 0.114 5.00e-02 4.00e+02 pdb=" CA PRO L 95 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO L 95 " -0.038 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS G 462 " -0.037 5.00e-02 4.00e+02 5.52e-02 4.88e+00 pdb=" N PRO G 463 " 0.096 5.00e-02 4.00e+02 pdb=" CA PRO G 463 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO G 463 " -0.031 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL L 58 " -0.036 5.00e-02 4.00e+02 5.44e-02 4.74e+00 pdb=" N PRO L 59 " 0.094 5.00e-02 4.00e+02 pdb=" CA PRO L 59 " -0.028 5.00e-02 4.00e+02 pdb=" CD PRO L 59 " -0.030 5.00e-02 4.00e+02 ... (remaining 908 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1629 2.82 - 3.34: 4043 3.34 - 3.86: 7954 3.86 - 4.38: 8799 4.38 - 4.90: 15817 Nonbonded interactions: 38242 Sorted by model distance: nonbonded pdb=" OD2 ASP G 398 " pdb=" OH TYR G 423 " model vdw 2.297 2.440 nonbonded pdb=" O SER B 91 " pdb=" OG SER B 91 " model vdw 2.307 2.440 nonbonded pdb=" OD1 ASP A 90 " pdb=" OH TYR A 94 " model vdw 2.314 2.440 nonbonded pdb=" OG1 THR G 345 " pdb=" O ASN B 92 " model vdw 2.327 2.440 nonbonded pdb=" OG SER B 63 " pdb=" OG SER B 74 " model vdw 2.332 2.440 ... (remaining 38237 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== 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=0.83 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: 9.440 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: 38.320 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 18.690 Find NCS groups from input model: 0.160 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: 0.010 Load rotamer database and sin/cos tables:2.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 69.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6776 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 : 0.007 0.068 5221 Z= 0.456 Angle : 0.878 10.910 7082 Z= 0.494 Chirality : 0.057 0.284 764 Planarity : 0.007 0.066 910 Dihedral : 15.145 100.082 1905 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 0.91 % Allowed : 9.80 % Favored : 89.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.73 (0.29), residues: 635 helix: -5.19 (0.23), residues: 20 sheet: -2.11 (0.31), residues: 238 loop : -2.64 (0.27), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP G 436 HIS 0.003 0.001 HIS L 91 PHE 0.020 0.002 PHE B 62 TYR 0.022 0.003 TYR L 49 ARG 0.003 0.001 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 0.569 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: G 466 ARG cc_start: 0.6802 (ptm160) cc_final: 0.5969 (ptm160) REVERT: G 472 ILE cc_start: 0.7949 (mm) cc_final: 0.7591 (mm) REVERT: G 493 GLN cc_start: 0.7198 (tt0) cc_final: 0.6725 (tm-30) REVERT: L 4 MET cc_start: 0.8176 (mmm) cc_final: 0.7958 (mmp) REVERT: L 19 VAL cc_start: 0.8552 (p) cc_final: 0.8208 (t) REVERT: L 26 SER cc_start: 0.7614 (m) cc_final: 0.7171 (m) REVERT: L 102 THR cc_start: 0.8308 (m) cc_final: 0.8092 (m) REVERT: H 35 ASP cc_start: 0.7719 (m-30) cc_final: 0.6547 (m-30) REVERT: H 50 GLN cc_start: 0.7769 (tt0) cc_final: 0.6865 (tt0) REVERT: H 54 LYS cc_start: 0.8345 (mtpt) cc_final: 0.7885 (tptt) REVERT: H 73 SER cc_start: 0.7672 (m) cc_final: 0.7458 (p) REVERT: B 40 SER cc_start: 0.7934 (t) cc_final: 0.7721 (t) REVERT: B 61 ARG cc_start: 0.6137 (ptt-90) cc_final: 0.5591 (ptt-90) REVERT: B 70 ASP cc_start: 0.7105 (m-30) cc_final: 0.6324 (m-30) REVERT: B 105 GLU cc_start: 0.7443 (pt0) cc_final: 0.7241 (pt0) REVERT: A 10 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7310 (mm-30) REVERT: A 19 LYS cc_start: 0.7808 (ttmt) cc_final: 0.7351 (tttp) REVERT: A 62 ASP cc_start: 0.7672 (m-30) cc_final: 0.7434 (m-30) REVERT: A 65 ARG cc_start: 0.7007 (ttp-110) cc_final: 0.6655 (mtm110) REVERT: A 87 LYS cc_start: 0.7568 (mttt) cc_final: 0.7239 (mtmt) outliers start: 5 outliers final: 5 residues processed: 158 average time/residue: 0.2077 time to fit residues: 40.1941 Evaluate side-chains 137 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 132 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 0.7980 chunk 31 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.4980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 chunk 55 optimal weight: 0.8980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 370 ASN G 440 ASN G 460 ASN L 8 GLN L 37 GLN L 38 GLN L 77 ASN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 50 GLN H 111 GLN B 27 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 53 GLN A 52 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6699 moved from start: 0.1497 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 5221 Z= 0.268 Angle : 0.599 7.609 7082 Z= 0.318 Chirality : 0.045 0.152 764 Planarity : 0.005 0.051 910 Dihedral : 8.759 59.919 773 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 9.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.83 % Favored : 94.17 % Rotamer: Outliers : 3.99 % Allowed : 18.51 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.34 (0.31), residues: 635 helix: -4.74 (0.43), residues: 26 sheet: -1.82 (0.31), residues: 265 loop : -2.32 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP G 436 HIS 0.002 0.001 HIS L 91 PHE 0.013 0.001 PHE B 62 TYR 0.020 0.002 TYR L 49 ARG 0.003 0.000 ARG L 18 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 140 time to evaluate : 0.624 Fit side-chains revert: symmetry clash REVERT: G 359 SER cc_start: 0.8585 (t) cc_final: 0.8239 (m) REVERT: G 466 ARG cc_start: 0.6921 (ptm160) cc_final: 0.6046 (ptm160) REVERT: G 472 ILE cc_start: 0.8032 (mm) cc_final: 0.7624 (mm) REVERT: G 483 VAL cc_start: 0.8065 (t) cc_final: 0.7689 (m) REVERT: G 484 GLU cc_start: 0.8727 (mt-10) cc_final: 0.8487 (mt-10) REVERT: L 26 SER cc_start: 0.7780 (m) cc_final: 0.7444 (m) REVERT: L 104 LEU cc_start: 0.5446 (OUTLIER) cc_final: 0.5100 (tt) REVERT: H 73 SER cc_start: 0.7599 (m) cc_final: 0.7363 (p) REVERT: H 108 PHE cc_start: 0.7901 (t80) cc_final: 0.7553 (t80) REVERT: B 61 ARG cc_start: 0.6170 (ptt-90) cc_final: 0.5783 (ptt-90) REVERT: A 10 GLU cc_start: 0.7583 (mm-30) cc_final: 0.7260 (mm-30) REVERT: A 19 LYS cc_start: 0.7390 (ttmt) cc_final: 0.7100 (tttt) REVERT: A 43 LYS cc_start: 0.7348 (mppt) cc_final: 0.6849 (mptt) REVERT: A 63 GLU cc_start: 0.8871 (tt0) cc_final: 0.8642 (tt0) REVERT: A 65 ARG cc_start: 0.6845 (ttp-110) cc_final: 0.6382 (ttm110) REVERT: A 87 LYS cc_start: 0.7494 (mttt) cc_final: 0.7152 (mtmt) outliers start: 22 outliers final: 19 residues processed: 151 average time/residue: 0.1974 time to fit residues: 36.8939 Evaluate side-chains 149 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 129 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 417 LYS Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain B residue 75 ILE Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 30 THR Chi-restraints excluded: chain A residue 55 SER Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 chunk 55 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 49 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 54 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 39 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6703 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.066 5221 Z= 0.293 Angle : 0.597 6.913 7082 Z= 0.312 Chirality : 0.044 0.152 764 Planarity : 0.004 0.041 910 Dihedral : 6.989 36.421 770 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.93 % Favored : 93.07 % Rotamer: Outliers : 5.63 % Allowed : 20.51 % Favored : 73.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.10 (0.32), residues: 635 helix: -4.36 (0.59), residues: 26 sheet: -1.63 (0.32), residues: 262 loop : -2.21 (0.31), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP G 436 HIS 0.002 0.001 HIS H 58 PHE 0.014 0.001 PHE B 62 TYR 0.019 0.002 TYR L 49 ARG 0.002 0.000 ARG H 52 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 136 time to evaluate : 0.598 Fit side-chains revert: symmetry clash REVERT: G 359 SER cc_start: 0.8514 (t) cc_final: 0.8208 (m) REVERT: G 417 LYS cc_start: 0.7453 (OUTLIER) cc_final: 0.6671 (tttp) REVERT: G 466 ARG cc_start: 0.6880 (ptm160) cc_final: 0.6008 (ptm160) REVERT: G 472 ILE cc_start: 0.8054 (mm) cc_final: 0.7638 (mm) REVERT: G 481 ASN cc_start: 0.8661 (t0) cc_final: 0.8408 (t0) REVERT: G 483 VAL cc_start: 0.8047 (t) cc_final: 0.7710 (m) REVERT: G 484 GLU cc_start: 0.8704 (mt-10) cc_final: 0.8484 (mt-10) REVERT: L 4 MET cc_start: 0.8399 (mmp) cc_final: 0.8150 (mmp) REVERT: L 26 SER cc_start: 0.7856 (m) cc_final: 0.7636 (m) REVERT: L 104 LEU cc_start: 0.5505 (OUTLIER) cc_final: 0.5080 (tt) REVERT: H 73 SER cc_start: 0.7586 (m) cc_final: 0.7369 (p) REVERT: H 89 ARG cc_start: 0.7724 (tpt90) cc_final: 0.7321 (tpt90) REVERT: H 102 MET cc_start: 0.8161 (mmm) cc_final: 0.7765 (mmm) REVERT: H 108 PHE cc_start: 0.7977 (t80) cc_final: 0.7606 (t80) REVERT: B 61 ARG cc_start: 0.6087 (ptt-90) cc_final: 0.5555 (ptt-90) REVERT: B 105 GLU cc_start: 0.7327 (pt0) cc_final: 0.7100 (pt0) REVERT: A 10 GLU cc_start: 0.7544 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 19 LYS cc_start: 0.7374 (ttmt) cc_final: 0.7063 (tttt) REVERT: A 65 ARG cc_start: 0.6903 (ttp-110) cc_final: 0.6056 (ttm-80) outliers start: 31 outliers final: 25 residues processed: 150 average time/residue: 0.1822 time to fit residues: 34.2717 Evaluate side-chains 158 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 131 time to evaluate : 0.613 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 417 LYS Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 511 VAL Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain L residue 89 LEU Chi-restraints excluded: chain L residue 104 LEU Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 92 ASN Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 37 optimal weight: 0.0170 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.0970 chunk 29 optimal weight: 5.9990 chunk 52 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 49 optimal weight: 0.0370 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 55 HIS ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6655 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5221 Z= 0.147 Angle : 0.516 6.195 7082 Z= 0.272 Chirality : 0.042 0.147 764 Planarity : 0.004 0.044 910 Dihedral : 5.806 34.956 770 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.67 % Favored : 94.33 % Rotamer: Outliers : 4.90 % Allowed : 21.42 % Favored : 73.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.88 (0.32), residues: 635 helix: -4.17 (0.68), residues: 26 sheet: -1.40 (0.32), residues: 248 loop : -2.13 (0.31), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP G 436 HIS 0.002 0.001 HIS H 58 PHE 0.016 0.001 PHE L 62 TYR 0.018 0.001 TYR A 105 ARG 0.004 0.000 ARG G 408 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 138 time to evaluate : 0.602 Fit side-chains REVERT: G 359 SER cc_start: 0.8390 (t) cc_final: 0.8108 (m) REVERT: G 417 LYS cc_start: 0.7404 (OUTLIER) cc_final: 0.7148 (tppt) REVERT: G 466 ARG cc_start: 0.6814 (ptm160) cc_final: 0.5963 (ptm160) REVERT: G 472 ILE cc_start: 0.8055 (mm) cc_final: 0.7623 (mm) REVERT: G 481 ASN cc_start: 0.8675 (t0) cc_final: 0.8338 (t0) REVERT: G 484 GLU cc_start: 0.8718 (mt-10) cc_final: 0.8498 (mt-10) REVERT: H 73 SER cc_start: 0.7575 (m) cc_final: 0.7344 (p) REVERT: H 89 ARG cc_start: 0.7642 (tpt90) cc_final: 0.7230 (tpt90) REVERT: H 102 MET cc_start: 0.8173 (mmm) cc_final: 0.7745 (mmm) REVERT: H 108 PHE cc_start: 0.8131 (t80) cc_final: 0.7640 (t80) REVERT: B 61 ARG cc_start: 0.5941 (ptt-90) cc_final: 0.5353 (ptt90) REVERT: A 10 GLU cc_start: 0.7534 (mm-30) cc_final: 0.7215 (mm-30) REVERT: A 19 LYS cc_start: 0.7335 (ttmt) cc_final: 0.7041 (ttpt) REVERT: A 43 LYS cc_start: 0.7196 (mppt) cc_final: 0.6706 (mptt) REVERT: A 63 GLU cc_start: 0.8823 (tt0) cc_final: 0.8605 (tt0) REVERT: A 65 ARG cc_start: 0.6791 (ttp-110) cc_final: 0.6583 (ttm-80) outliers start: 27 outliers final: 18 residues processed: 150 average time/residue: 0.1798 time to fit residues: 34.1104 Evaluate side-chains 149 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 130 time to evaluate : 0.591 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 417 LYS Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 30 optimal weight: 2.9990 chunk 52 optimal weight: 0.6980 chunk 14 optimal weight: 1.9990 chunk 19 optimal weight: 0.0060 chunk 53 optimal weight: 0.5980 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6666 moved from start: 0.2495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 5221 Z= 0.215 Angle : 0.544 6.355 7082 Z= 0.281 Chirality : 0.043 0.149 764 Planarity : 0.004 0.046 910 Dihedral : 5.747 34.038 770 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.53 % Allowed : 22.32 % Favored : 71.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.70 (0.32), residues: 635 helix: -4.10 (0.72), residues: 26 sheet: -1.25 (0.33), residues: 246 loop : -2.03 (0.31), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP G 436 HIS 0.002 0.001 HIS H 58 PHE 0.010 0.001 PHE A 64 TYR 0.016 0.001 TYR L 49 ARG 0.002 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 133 time to evaluate : 0.589 Fit side-chains revert: symmetry clash REVERT: G 359 SER cc_start: 0.8417 (t) cc_final: 0.8145 (m) REVERT: G 466 ARG cc_start: 0.6817 (ptm160) cc_final: 0.5933 (ptm160) REVERT: G 472 ILE cc_start: 0.8048 (mm) cc_final: 0.7629 (mm) REVERT: G 481 ASN cc_start: 0.8695 (t0) cc_final: 0.8298 (t0) REVERT: G 484 GLU cc_start: 0.8731 (mt-10) cc_final: 0.8515 (mt-10) REVERT: L 47 MET cc_start: 0.7033 (OUTLIER) cc_final: 0.6644 (mmm) REVERT: L 107 LYS cc_start: 0.5248 (mtmm) cc_final: 0.4896 (mmtt) REVERT: H 73 SER cc_start: 0.7569 (m) cc_final: 0.7340 (p) REVERT: H 89 ARG cc_start: 0.7611 (tpt90) cc_final: 0.7257 (tpt90) REVERT: H 102 MET cc_start: 0.8155 (mmm) cc_final: 0.7681 (mmm) REVERT: H 108 PHE cc_start: 0.8081 (t80) cc_final: 0.7621 (t80) REVERT: B 61 ARG cc_start: 0.6000 (ptt-90) cc_final: 0.5339 (ptt-90) REVERT: B 90 GLN cc_start: 0.8113 (pp30) cc_final: 0.7147 (pp30) REVERT: B 105 GLU cc_start: 0.7311 (pt0) cc_final: 0.7099 (pt0) REVERT: A 10 GLU cc_start: 0.7547 (mm-30) cc_final: 0.7297 (mm-30) REVERT: A 19 LYS cc_start: 0.7351 (ttmt) cc_final: 0.7036 (tttt) REVERT: A 43 LYS cc_start: 0.7178 (mppt) cc_final: 0.6688 (mptt) REVERT: A 63 GLU cc_start: 0.8815 (tt0) cc_final: 0.8608 (tt0) outliers start: 36 outliers final: 28 residues processed: 149 average time/residue: 0.1823 time to fit residues: 34.2700 Evaluate side-chains 162 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 133 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 402 ILE Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 47 MET Chi-restraints excluded: chain L residue 60 ASP Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 37 GLN Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 51 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 14 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.4980 chunk 56 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6683 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.074 5221 Z= 0.309 Angle : 0.590 6.696 7082 Z= 0.303 Chirality : 0.044 0.156 764 Planarity : 0.004 0.045 910 Dihedral : 5.979 32.927 770 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 11.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 6.53 % Allowed : 23.05 % Favored : 70.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.65 (0.32), residues: 635 helix: -3.70 (0.91), residues: 20 sheet: -1.21 (0.31), residues: 260 loop : -2.10 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.002 0.001 HIS H 58 PHE 0.014 0.001 PHE B 62 TYR 0.025 0.002 TYR G 453 ARG 0.002 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 128 time to evaluate : 0.521 Fit side-chains REVERT: G 359 SER cc_start: 0.8503 (t) cc_final: 0.8224 (m) REVERT: G 408 ARG cc_start: 0.8322 (ttp80) cc_final: 0.8054 (ttp80) REVERT: G 466 ARG cc_start: 0.6924 (ptm160) cc_final: 0.5934 (ptm160) REVERT: G 472 ILE cc_start: 0.8083 (mm) cc_final: 0.7673 (mm) REVERT: G 481 ASN cc_start: 0.8771 (t0) cc_final: 0.8316 (t0) REVERT: G 484 GLU cc_start: 0.8742 (mt-10) cc_final: 0.8524 (mt-10) REVERT: L 4 MET cc_start: 0.8242 (mmp) cc_final: 0.7973 (mmp) REVERT: L 107 LYS cc_start: 0.5232 (mtmm) cc_final: 0.4949 (mmtt) REVERT: H 73 SER cc_start: 0.7535 (m) cc_final: 0.7315 (p) REVERT: H 89 ARG cc_start: 0.7716 (tpt90) cc_final: 0.7348 (tpt90) REVERT: H 102 MET cc_start: 0.8119 (mmm) cc_final: 0.7816 (mmm) REVERT: H 108 PHE cc_start: 0.8072 (t80) cc_final: 0.7670 (t80) REVERT: B 61 ARG cc_start: 0.6038 (ptt-90) cc_final: 0.5326 (ptt-90) REVERT: B 105 GLU cc_start: 0.7291 (pt0) cc_final: 0.7061 (pt0) REVERT: A 19 LYS cc_start: 0.7433 (ttmt) cc_final: 0.7100 (tttt) REVERT: A 65 ARG cc_start: 0.6912 (ttp-110) cc_final: 0.6699 (ttm-80) outliers start: 36 outliers final: 29 residues processed: 148 average time/residue: 0.1769 time to fit residues: 33.2035 Evaluate side-chains 156 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 127 time to evaluate : 0.576 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 58 optimal weight: 0.0970 chunk 36 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.7980 chunk 11 optimal weight: 0.9980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN L 37 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6669 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 5221 Z= 0.228 Angle : 0.558 5.816 7082 Z= 0.287 Chirality : 0.044 0.161 764 Planarity : 0.003 0.046 910 Dihedral : 5.731 32.641 770 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 10.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 5.99 % Allowed : 24.68 % Favored : 69.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.54 (0.32), residues: 635 helix: -3.67 (0.92), residues: 20 sheet: -1.13 (0.31), residues: 260 loop : -2.01 (0.32), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP G 436 HIS 0.004 0.001 HIS H 58 PHE 0.009 0.001 PHE B 62 TYR 0.019 0.001 TYR G 453 ARG 0.002 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 131 time to evaluate : 0.565 Fit side-chains revert: symmetry clash REVERT: G 359 SER cc_start: 0.8413 (t) cc_final: 0.8166 (m) REVERT: G 408 ARG cc_start: 0.8293 (ttp80) cc_final: 0.8033 (ttp80) REVERT: G 466 ARG cc_start: 0.6834 (ptm160) cc_final: 0.5907 (ptm160) REVERT: G 472 ILE cc_start: 0.8065 (mm) cc_final: 0.7654 (mm) REVERT: G 484 GLU cc_start: 0.8747 (mt-10) cc_final: 0.8538 (mt-10) REVERT: L 4 MET cc_start: 0.8221 (mmp) cc_final: 0.7914 (mmp) REVERT: L 47 MET cc_start: 0.7269 (mmm) cc_final: 0.7006 (tpp) REVERT: L 62 PHE cc_start: 0.7371 (m-80) cc_final: 0.7138 (m-10) REVERT: L 107 LYS cc_start: 0.5335 (mtmm) cc_final: 0.5033 (mmtt) REVERT: H 73 SER cc_start: 0.7515 (m) cc_final: 0.7306 (p) REVERT: H 89 ARG cc_start: 0.7684 (tpt90) cc_final: 0.7319 (tpt90) REVERT: H 102 MET cc_start: 0.8114 (mmm) cc_final: 0.7803 (mmm) REVERT: H 108 PHE cc_start: 0.8057 (t80) cc_final: 0.7669 (t80) REVERT: B 61 ARG cc_start: 0.6043 (ptt-90) cc_final: 0.5721 (ptt90) REVERT: B 90 GLN cc_start: 0.8014 (pp30) cc_final: 0.7119 (pp30) REVERT: B 105 GLU cc_start: 0.7339 (pt0) cc_final: 0.7107 (pt0) REVERT: A 65 ARG cc_start: 0.6757 (ttp-110) cc_final: 0.5959 (ttm-80) outliers start: 33 outliers final: 30 residues processed: 152 average time/residue: 0.1901 time to fit residues: 36.3879 Evaluate side-chains 157 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 127 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 31 ASP Chi-restraints excluded: chain H residue 35 ASP Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 0.9990 chunk 37 optimal weight: 1.9990 chunk 40 optimal weight: 0.4980 chunk 29 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 46 optimal weight: 2.9990 chunk 53 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 27 GLN ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6676 moved from start: 0.2748 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 5221 Z= 0.279 Angle : 0.577 6.330 7082 Z= 0.297 Chirality : 0.044 0.162 764 Planarity : 0.004 0.046 910 Dihedral : 5.830 32.508 770 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 11.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer: Outliers : 6.53 % Allowed : 25.05 % Favored : 68.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.50 (0.32), residues: 635 helix: -4.02 (0.72), residues: 26 sheet: -1.08 (0.32), residues: 260 loop : -1.93 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 104 HIS 0.004 0.001 HIS H 58 PHE 0.042 0.002 PHE H 70 TYR 0.020 0.002 TYR G 453 ARG 0.002 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 0.602 Fit side-chains revert: symmetry clash REVERT: G 359 SER cc_start: 0.8454 (t) cc_final: 0.8206 (m) REVERT: G 408 ARG cc_start: 0.8315 (ttp80) cc_final: 0.8048 (ttp80) REVERT: G 466 ARG cc_start: 0.6799 (ptm160) cc_final: 0.5881 (ptm160) REVERT: G 472 ILE cc_start: 0.8051 (mm) cc_final: 0.7648 (mm) REVERT: G 481 ASN cc_start: 0.8674 (OUTLIER) cc_final: 0.8329 (p0) REVERT: G 484 GLU cc_start: 0.8749 (mt-10) cc_final: 0.8391 (mt-10) REVERT: L 4 MET cc_start: 0.8175 (mmp) cc_final: 0.7856 (mmp) REVERT: L 47 MET cc_start: 0.7315 (mmm) cc_final: 0.6734 (tpp) REVERT: L 62 PHE cc_start: 0.7371 (m-80) cc_final: 0.7154 (m-10) REVERT: L 107 LYS cc_start: 0.5357 (mtmm) cc_final: 0.5057 (mmtt) REVERT: H 73 SER cc_start: 0.7484 (m) cc_final: 0.7281 (p) REVERT: H 89 ARG cc_start: 0.7692 (tpt90) cc_final: 0.7311 (tpt90) REVERT: H 102 MET cc_start: 0.8091 (mmm) cc_final: 0.7745 (mmm) REVERT: H 108 PHE cc_start: 0.8085 (t80) cc_final: 0.7729 (t80) REVERT: B 61 ARG cc_start: 0.6060 (ptt-90) cc_final: 0.5708 (ptt90) REVERT: B 90 GLN cc_start: 0.8018 (pp30) cc_final: 0.7120 (pp30) REVERT: B 105 GLU cc_start: 0.7311 (pt0) cc_final: 0.7083 (pt0) REVERT: A 65 ARG cc_start: 0.6738 (ttp-110) cc_final: 0.5945 (ttm-80) outliers start: 36 outliers final: 32 residues processed: 151 average time/residue: 0.1864 time to fit residues: 35.7030 Evaluate side-chains 161 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 128 time to evaluate : 0.615 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 481 ASN Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 30 SER Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 0.0010 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.7980 chunk 49 optimal weight: 0.2980 chunk 51 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 chunk 35 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 60 optimal weight: 0.1980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN A 101 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.2882 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5221 Z= 0.185 Angle : 0.534 5.523 7082 Z= 0.276 Chirality : 0.043 0.163 764 Planarity : 0.003 0.048 910 Dihedral : 5.481 32.723 770 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.14 % Favored : 93.86 % Rotamer: Outliers : 6.90 % Allowed : 24.50 % Favored : 68.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.39 (0.32), residues: 635 helix: -3.99 (0.73), residues: 26 sheet: -0.99 (0.33), residues: 250 loop : -1.85 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 104 HIS 0.003 0.001 HIS H 58 PHE 0.028 0.001 PHE H 70 TYR 0.017 0.001 TYR A 105 ARG 0.002 0.000 ARG G 355 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 132 time to evaluate : 0.587 Fit side-chains revert: symmetry clash REVERT: G 359 SER cc_start: 0.8372 (t) cc_final: 0.8158 (m) REVERT: G 408 ARG cc_start: 0.8292 (ttp80) cc_final: 0.8034 (ttp80) REVERT: G 466 ARG cc_start: 0.6742 (ptm160) cc_final: 0.5844 (ptm160) REVERT: G 472 ILE cc_start: 0.8046 (mm) cc_final: 0.7647 (mm) REVERT: G 481 ASN cc_start: 0.8661 (OUTLIER) cc_final: 0.8374 (p0) REVERT: G 484 GLU cc_start: 0.8754 (mt-10) cc_final: 0.8406 (mt-10) REVERT: L 4 MET cc_start: 0.8117 (mmp) cc_final: 0.7806 (mmp) REVERT: L 14 SER cc_start: 0.7182 (t) cc_final: 0.6742 (p) REVERT: L 47 MET cc_start: 0.7209 (mmm) cc_final: 0.6990 (tpp) REVERT: L 107 LYS cc_start: 0.5444 (mtmm) cc_final: 0.5063 (mmtt) REVERT: H 73 SER cc_start: 0.7461 (m) cc_final: 0.7260 (p) REVERT: H 89 ARG cc_start: 0.7646 (tpt90) cc_final: 0.7272 (tpt90) REVERT: H 102 MET cc_start: 0.8101 (mmm) cc_final: 0.7784 (mmm) REVERT: H 108 PHE cc_start: 0.8064 (t80) cc_final: 0.7718 (t80) REVERT: B 61 ARG cc_start: 0.6035 (ptt-90) cc_final: 0.5659 (ptt90) REVERT: B 90 GLN cc_start: 0.8029 (pp30) cc_final: 0.7127 (pp30) REVERT: B 105 GLU cc_start: 0.7284 (pt0) cc_final: 0.7060 (pt0) REVERT: A 101 ASN cc_start: 0.8468 (OUTLIER) cc_final: 0.8183 (t0) outliers start: 38 outliers final: 34 residues processed: 151 average time/residue: 0.1815 time to fit residues: 34.7654 Evaluate side-chains 166 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 130 time to evaluate : 0.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 441 LEU Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 481 ASN Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Chi-restraints excluded: chain A residue 101 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 5.9990 chunk 38 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 0.9990 chunk 44 optimal weight: 0.8980 chunk 7 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN ** B 34 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 88 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6674 moved from start: 0.2928 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 5221 Z= 0.307 Angle : 0.573 5.742 7082 Z= 0.295 Chirality : 0.044 0.160 764 Planarity : 0.004 0.047 910 Dihedral : 5.632 32.443 770 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.40 % Favored : 92.60 % Rotamer: Outliers : 6.90 % Allowed : 24.14 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.37 (0.33), residues: 635 helix: -3.99 (0.73), residues: 26 sheet: -0.98 (0.33), residues: 250 loop : -1.85 (0.32), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP G 436 HIS 0.002 0.001 HIS H 58 PHE 0.024 0.002 PHE H 70 TYR 0.019 0.002 TYR G 453 ARG 0.007 0.000 ARG A 65 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1270 Ramachandran restraints generated. 635 Oldfield, 0 Emsley, 635 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 168 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 130 time to evaluate : 0.600 Fit side-chains revert: symmetry clash REVERT: G 359 SER cc_start: 0.8402 (t) cc_final: 0.8177 (m) REVERT: G 408 ARG cc_start: 0.8316 (ttp80) cc_final: 0.8065 (ttp80) REVERT: G 466 ARG cc_start: 0.6788 (ptm160) cc_final: 0.5859 (ptm160) REVERT: G 472 ILE cc_start: 0.8043 (mm) cc_final: 0.7645 (mm) REVERT: G 481 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.8371 (p0) REVERT: G 484 GLU cc_start: 0.8760 (mt-10) cc_final: 0.8409 (mt-10) REVERT: L 4 MET cc_start: 0.8132 (mmp) cc_final: 0.7823 (mmp) REVERT: L 8 GLN cc_start: 0.5168 (mp10) cc_final: 0.4719 (mp10) REVERT: L 14 SER cc_start: 0.7204 (t) cc_final: 0.6757 (p) REVERT: L 47 MET cc_start: 0.7333 (mmm) cc_final: 0.6713 (tpp) REVERT: L 107 LYS cc_start: 0.5353 (mtmm) cc_final: 0.4991 (mmtt) REVERT: H 89 ARG cc_start: 0.7673 (tpt90) cc_final: 0.7294 (tpt90) REVERT: H 102 MET cc_start: 0.8104 (mmm) cc_final: 0.7757 (mmm) REVERT: H 106 MET cc_start: 0.7365 (mmm) cc_final: 0.7140 (mpp) REVERT: H 108 PHE cc_start: 0.8058 (t80) cc_final: 0.7702 (t80) REVERT: B 61 ARG cc_start: 0.6076 (ptt-90) cc_final: 0.5685 (ptt90) REVERT: B 90 GLN cc_start: 0.7954 (pp30) cc_final: 0.7066 (pp30) REVERT: B 105 GLU cc_start: 0.7332 (pt0) cc_final: 0.7109 (pt0) REVERT: A 65 ARG cc_start: 0.7152 (ttm-80) cc_final: 0.6920 (ttm-80) outliers start: 38 outliers final: 33 residues processed: 150 average time/residue: 0.1879 time to fit residues: 35.5963 Evaluate side-chains 163 residues out of total 551 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 129 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain G residue 349 SER Chi-restraints excluded: chain G residue 367 VAL Chi-restraints excluded: chain G residue 395 VAL Chi-restraints excluded: chain G residue 398 ASP Chi-restraints excluded: chain G residue 430 THR Chi-restraints excluded: chain G residue 470 THR Chi-restraints excluded: chain G residue 481 ASN Chi-restraints excluded: chain G residue 495 TYR Chi-restraints excluded: chain G residue 501 ASN Chi-restraints excluded: chain G residue 512 VAL Chi-restraints excluded: chain L residue 29 VAL Chi-restraints excluded: chain L residue 33 VAL Chi-restraints excluded: chain L residue 70 ASP Chi-restraints excluded: chain L residue 72 THR Chi-restraints excluded: chain L residue 78 VAL Chi-restraints excluded: chain L residue 85 ASP Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 5 GLU Chi-restraints excluded: chain H residue 34 MET Chi-restraints excluded: chain H residue 37 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 115 VAL Chi-restraints excluded: chain B residue 14 THR Chi-restraints excluded: chain B residue 69 THR Chi-restraints excluded: chain B residue 83 PHE Chi-restraints excluded: chain B residue 93 THR Chi-restraints excluded: chain B residue 97 THR Chi-restraints excluded: chain A residue 2 ILE Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 17 THR Chi-restraints excluded: chain A residue 35 ASN Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 74 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 42 optimal weight: 0.0570 chunk 2 optimal weight: 0.7980 chunk 35 optimal weight: 0.0980 chunk 55 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 41 optimal weight: 0.3980 overall best weight: 0.3498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 91 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 111 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3323 r_free = 0.3323 target = 0.121900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3086 r_free = 0.3086 target = 0.104144 restraints weight = 7833.439| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.106525 restraints weight = 5324.093| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.108196 restraints weight = 4050.445| |-----------------------------------------------------------------------------| r_work (final): 0.3147 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3146 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.83 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3146 r_free = 0.3146 target_work(ls_wunit_k1) = 0.108 | | occupancies: max = 1.00 min = 0.35 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3146 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8265 moved from start: 0.3069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5221 Z= 0.162 Angle : 0.529 5.498 7082 Z= 0.274 Chirality : 0.043 0.162 764 Planarity : 0.004 0.048 910 Dihedral : 5.335 32.616 770 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer: Outliers : 6.35 % Allowed : 24.68 % Favored : 68.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.22 (0.33), residues: 635 helix: -3.48 (0.76), residues: 32 sheet: -0.90 (0.33), residues: 249 loop : -1.71 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP G 436 HIS 0.002 0.001 HIS H 58 PHE 0.020 0.001 PHE H 70 TYR 0.017 0.001 TYR A 105 ARG 0.006 0.000 ARG A 65 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1988.42 seconds wall clock time: 36 minutes 37.56 seconds (2197.56 seconds total)