Starting phenix.real_space_refine on Mon Feb 10 22:20:05 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7n5g_24189/02_2025/7n5g_24189.cif Found real_map, /net/cci-nas-00/data/ceres_data/7n5g_24189/02_2025/7n5g_24189.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7n5g_24189/02_2025/7n5g_24189.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7n5g_24189/02_2025/7n5g_24189.map" model { file = "/net/cci-nas-00/data/ceres_data/7n5g_24189/02_2025/7n5g_24189.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7n5g_24189/02_2025/7n5g_24189.cif" } resolution = 2.4 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= 0.023 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 12 5.16 5 C 1920 2.51 5 N 486 2.21 5 O 508 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 2926 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 2908 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2908 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 37} Link IDs: {'PTRANS': 7, 'TRANS': 363} Chain breaks: 4 Unresolved non-hydrogen bonds: 128 Unresolved non-hydrogen angles: 170 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 21 Planarities with less than four sites: {'PHE:plan': 3, 'GLU:plan': 1, 'TRP:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "B" Number of atoms: 18 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 18 Unusual residues: {'PLM': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.68, per 1000 atoms: 0.92 Number of scatterers: 2926 At special positions: 0 Unit cell: (70.04, 93.73, 140.08, 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 12 16.00 O 508 8.00 N 486 7.00 C 1920 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.75 Conformation dependent library (CDL) restraints added in 342.3 milliseconds 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 720 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 2 sheets defined 63.9% alpha, 11.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.33 Creating SS restraints... Processing helix chain 'B' and resid 186 through 203 Processing helix chain 'B' and resid 223 through 232 Processing helix chain 'B' and resid 235 through 241 Processing helix chain 'B' and resid 265 through 285 Processing helix chain 'B' and resid 295 through 329 removed outlier: 3.824A pdb=" N LEU B 299 " --> pdb=" O THR B 295 " (cutoff:3.500A) removed outlier: 3.905A pdb=" N SER B 329 " --> pdb=" O ILE B 325 " (cutoff:3.500A) Processing helix chain 'B' and resid 330 through 331 No H-bonds generated for 'chain 'B' and resid 330 through 331' Processing helix chain 'B' and resid 332 through 334 No H-bonds generated for 'chain 'B' and resid 332 through 334' Processing helix chain 'B' and resid 335 through 349 Processing helix chain 'B' and resid 508 through 524 Processing helix chain 'B' and resid 526 through 552 Processing helix chain 'B' and resid 556 through 590 removed outlier: 5.467A pdb=" N ASN B 576 " --> pdb=" O PHE B 572 " (cutoff:3.500A) removed outlier: 5.843A pdb=" N THR B 577 " --> pdb=" O ILE B 573 " (cutoff:3.500A) Processing helix chain 'B' and resid 631 through 635 Processing helix chain 'B' and resid 661 through 678 Processing helix chain 'B' and resid 714 through 737 Processing sheet with id=AA1, first strand: chain 'B' and resid 626 through 630 removed outlier: 7.157A pdb=" N THR B 616 " --> pdb=" O MET B 612 " (cutoff:3.500A) removed outlier: 5.243A pdb=" N MET B 612 " --> pdb=" O THR B 616 " (cutoff:3.500A) removed outlier: 6.842A pdb=" N VAL B 618 " --> pdb=" O GLU B 610 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 649 through 657 removed outlier: 6.485A pdb=" N LYS B 699 " --> pdb=" O ILE B 694 " (cutoff:3.500A) removed outlier: 4.361A pdb=" N ILE B 694 " --> pdb=" O LYS B 699 " (cutoff:3.500A) removed outlier: 6.582A pdb=" N LYS B 701 " --> pdb=" O LYS B 692 " (cutoff:3.500A) 206 hydrogen bonds defined for protein. 612 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: 0.79 Time building geometry restraints manager: 0.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 675 1.32 - 1.44: 718 1.44 - 1.57: 1550 1.57 - 1.69: 16 1.69 - 1.81: 21 Bond restraints: 2980 Sorted by residual: bond pdb=" CD2 TRP B 507 " pdb=" CE3 TRP B 507 " ideal model delta sigma weight residual 1.398 1.503 -0.105 1.60e-02 3.91e+03 4.27e+01 bond pdb=" CZ2 TRP B 507 " pdb=" CH2 TRP B 507 " ideal model delta sigma weight residual 1.368 1.480 -0.112 1.90e-02 2.77e+03 3.46e+01 bond pdb=" CB ILE B 285 " pdb=" CG1 ILE B 285 " ideal model delta sigma weight residual 1.530 1.635 -0.105 2.00e-02 2.50e+03 2.77e+01 bond pdb=" CB TYR B 629 " pdb=" CG TYR B 629 " ideal model delta sigma weight residual 1.512 1.399 0.113 2.20e-02 2.07e+03 2.65e+01 bond pdb=" CB HIS B 345 " pdb=" CG HIS B 345 " ideal model delta sigma weight residual 1.497 1.428 0.069 1.40e-02 5.10e+03 2.46e+01 ... (remaining 2975 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.65: 3160 1.65 - 3.30: 695 3.30 - 4.95: 146 4.95 - 6.59: 33 6.59 - 8.24: 5 Bond angle restraints: 4039 Sorted by residual: angle pdb=" C HIS B 592 " pdb=" N PRO B 593 " pdb=" CA PRO B 593 " ideal model delta sigma weight residual 119.56 126.54 -6.98 1.01e+00 9.80e-01 4.78e+01 angle pdb=" C SER B 645 " pdb=" N PRO B 646 " pdb=" CA PRO B 646 " ideal model delta sigma weight residual 120.52 126.91 -6.39 9.90e-01 1.02e+00 4.17e+01 angle pdb=" C LEU B 743 " pdb=" N PRO B 744 " pdb=" CA PRO B 744 " ideal model delta sigma weight residual 119.85 126.24 -6.39 1.01e+00 9.80e-01 4.00e+01 angle pdb=" C GLN B 291 " pdb=" N PRO B 292 " pdb=" CA PRO B 292 " ideal model delta sigma weight residual 119.28 125.41 -6.13 1.10e+00 8.26e-01 3.11e+01 angle pdb=" N SER B 267 " pdb=" CA SER B 267 " pdb=" C SER B 267 " ideal model delta sigma weight residual 112.23 105.58 6.65 1.26e+00 6.30e-01 2.79e+01 ... (remaining 4034 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.33: 1685 14.33 - 28.65: 62 28.65 - 42.97: 7 42.97 - 57.30: 11 57.30 - 71.62: 6 Dihedral angle restraints: 1771 sinusoidal: 680 harmonic: 1091 Sorted by residual: dihedral pdb=" CA ASP B 657 " pdb=" CB ASP B 657 " pdb=" CG ASP B 657 " pdb=" OD1 ASP B 657 " ideal model delta sinusoidal sigma weight residual -30.00 -84.87 54.87 1 2.00e+01 2.50e-03 1.02e+01 dihedral pdb=" CA ASP B 595 " pdb=" CB ASP B 595 " pdb=" CG ASP B 595 " pdb=" OD1 ASP B 595 " ideal model delta sinusoidal sigma weight residual -30.00 -74.43 44.43 1 2.00e+01 2.50e-03 6.86e+00 dihedral pdb=" N ASP B 650 " pdb=" C ASP B 650 " pdb=" CA ASP B 650 " pdb=" CB ASP B 650 " ideal model delta harmonic sigma weight residual 122.80 116.39 6.41 0 2.50e+00 1.60e-01 6.57e+00 ... (remaining 1768 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.097: 371 0.097 - 0.193: 99 0.193 - 0.290: 16 0.290 - 0.387: 3 0.387 - 0.483: 2 Chirality restraints: 491 Sorted by residual: chirality pdb=" CG LEU B 264 " pdb=" CB LEU B 264 " pdb=" CD1 LEU B 264 " pdb=" CD2 LEU B 264 " both_signs ideal model delta sigma weight residual False -2.59 -3.07 0.48 2.00e-01 2.50e+01 5.84e+00 chirality pdb=" CB ILE B 285 " pdb=" CA ILE B 285 " pdb=" CG1 ILE B 285 " pdb=" CG2 ILE B 285 " both_signs ideal model delta sigma weight residual False 2.64 3.05 -0.40 2.00e-01 2.50e+01 4.06e+00 chirality pdb=" CA TRP B 304 " pdb=" N TRP B 304 " pdb=" C TRP B 304 " pdb=" CB TRP B 304 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.19e+00 ... (remaining 488 not shown) Planarity restraints: 493 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA VAL B 697 " 0.015 2.00e-02 2.50e+03 3.07e-02 9.41e+00 pdb=" C VAL B 697 " -0.053 2.00e-02 2.50e+03 pdb=" O VAL B 697 " 0.020 2.00e-02 2.50e+03 pdb=" N ASN B 698 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 675 " 0.035 2.00e-02 2.50e+03 1.98e-02 7.85e+00 pdb=" CG TYR B 675 " -0.010 2.00e-02 2.50e+03 pdb=" CD1 TYR B 675 " -0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 675 " -0.012 2.00e-02 2.50e+03 pdb=" CE1 TYR B 675 " -0.011 2.00e-02 2.50e+03 pdb=" CE2 TYR B 675 " -0.013 2.00e-02 2.50e+03 pdb=" CZ TYR B 675 " -0.005 2.00e-02 2.50e+03 pdb=" OH TYR B 675 " 0.033 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASN B 741 " -0.012 2.00e-02 2.50e+03 2.42e-02 5.86e+00 pdb=" C ASN B 741 " 0.042 2.00e-02 2.50e+03 pdb=" O ASN B 741 " -0.016 2.00e-02 2.50e+03 pdb=" N LEU B 742 " -0.014 2.00e-02 2.50e+03 ... (remaining 490 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 1125 2.89 - 3.39: 2994 3.39 - 3.89: 4759 3.89 - 4.40: 5429 4.40 - 4.90: 8451 Nonbonded interactions: 22758 Sorted by model distance: nonbonded pdb=" OD1 ASP B 737 " pdb=" NZ LYS B 739 " model vdw 2.386 3.120 nonbonded pdb=" N VAL B 697 " pdb=" N ASN B 698 " model vdw 2.467 2.560 nonbonded pdb=" N ASN B 711 " pdb=" O ASN B 711 " model vdw 2.498 2.496 nonbonded pdb=" N PRO B 646 " pdb=" O PRO B 646 " model vdw 2.533 2.496 nonbonded pdb=" N ASN B 613 " pdb=" O ASN B 613 " model vdw 2.553 2.496 ... (remaining 22753 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 12.440 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 25.380 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7577 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 : 0.022 0.132 2980 Z= 1.484 Angle : 1.511 8.243 4039 Z= 1.034 Chirality : 0.093 0.483 491 Planarity : 0.008 0.031 493 Dihedral : 10.569 71.622 1051 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 0.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.41), residues: 361 helix: 1.41 (0.30), residues: 223 sheet: 0.94 (0.88), residues: 42 loop : 1.21 (0.65), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.008 TRP B 683 HIS 0.005 0.002 HIS B 346 PHE 0.019 0.005 PHE B 682 TYR 0.035 0.008 TYR B 675 ARG 0.005 0.001 ARG B 338 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 99 time to evaluate : 0.306 Fit side-chains revert: symmetry clash REVERT: B 526 LYS cc_start: 0.7984 (mttt) cc_final: 0.7595 (mtpp) REVERT: B 624 LYS cc_start: 0.8434 (mmtm) cc_final: 0.7572 (tttp) REVERT: B 702 MET cc_start: 0.8860 (mtt) cc_final: 0.8638 (mtp) outliers start: 0 outliers final: 1 residues processed: 99 average time/residue: 1.1784 time to fit residues: 119.5412 Evaluate side-chains 85 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 84 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 560 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.0050 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 9 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 6.9990 chunk 17 optimal weight: 0.8980 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 605 ASN B 648 GLN B 688 ASN B 698 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160441 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3866 r_free = 0.3866 target = 0.133768 restraints weight = 4006.760| |-----------------------------------------------------------------------------| r_work (start): 0.3862 rms_B_bonded: 1.66 r_work: 0.3740 rms_B_bonded: 2.39 restraints_weight: 0.5000 r_work: 0.3603 rms_B_bonded: 4.09 restraints_weight: 0.2500 r_work (final): 0.3603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2469 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2980 Z= 0.189 Angle : 0.488 6.378 4039 Z= 0.262 Chirality : 0.041 0.144 491 Planarity : 0.003 0.040 493 Dihedral : 8.461 54.637 397 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 4.56 % Allowed : 9.12 % Favored : 86.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.43), residues: 361 helix: 2.50 (0.32), residues: 229 sheet: 0.48 (0.76), residues: 42 loop : 0.76 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 281 HIS 0.002 0.001 HIS B 592 PHE 0.012 0.002 PHE B 271 TYR 0.005 0.001 TYR B 740 ARG 0.004 0.001 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.351 Fit side-chains revert: symmetry clash REVERT: B 283 MET cc_start: 0.5753 (tpp) cc_final: 0.5441 (mmm) outliers start: 14 outliers final: 6 residues processed: 95 average time/residue: 1.2257 time to fit residues: 119.2802 Evaluate side-chains 91 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 264 LEU Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 541 ILE Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 32 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 14 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 688 ASN B 698 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4178 r_free = 0.4178 target = 0.159496 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3860 r_free = 0.3860 target = 0.133569 restraints weight = 3956.390| |-----------------------------------------------------------------------------| r_work (start): 0.3859 rms_B_bonded: 1.56 r_work: 0.3740 rms_B_bonded: 2.26 restraints_weight: 0.5000 r_work: 0.3610 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3610 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2980 Z= 0.195 Angle : 0.447 6.830 4039 Z= 0.239 Chirality : 0.039 0.135 491 Planarity : 0.003 0.029 493 Dihedral : 8.023 54.156 397 Min Nonbonded Distance : 2.619 Molprobity Statistics. All-atom Clashscore : 3.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.83 % Favored : 99.17 % Rotamer: Outliers : 3.26 % Allowed : 12.70 % Favored : 84.04 % 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: 3.08 (0.43), residues: 361 helix: 2.86 (0.32), residues: 229 sheet: 0.58 (0.76), residues: 42 loop : 0.63 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.010 0.002 PHE B 654 TYR 0.008 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 0.332 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8732 (mmtm) cc_final: 0.7628 (tmmt) outliers start: 10 outliers final: 6 residues processed: 93 average time/residue: 1.2086 time to fit residues: 115.2934 Evaluate side-chains 91 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 85 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 2 optimal weight: 4.9990 chunk 1 optimal weight: 8.9990 chunk 32 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 17 optimal weight: 0.7980 chunk 16 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 24 optimal weight: 1.9990 chunk 21 optimal weight: 0.0270 overall best weight: 0.6440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 688 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.160019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.133361 restraints weight = 4091.478| |-----------------------------------------------------------------------------| r_work (start): 0.3855 rms_B_bonded: 1.60 r_work: 0.3740 rms_B_bonded: 2.24 restraints_weight: 0.5000 r_work: 0.3607 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3607 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7733 moved from start: 0.3228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2980 Z= 0.184 Angle : 0.439 7.062 4039 Z= 0.229 Chirality : 0.039 0.139 491 Planarity : 0.002 0.030 493 Dihedral : 7.772 55.225 397 Min Nonbonded Distance : 2.574 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.23 % Allowed : 13.68 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.44), residues: 361 helix: 3.05 (0.32), residues: 229 sheet: 0.64 (0.78), residues: 42 loop : 0.41 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.004 0.001 HIS B 708 PHE 0.011 0.001 PHE B 271 TYR 0.007 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: B 624 LYS cc_start: 0.8782 (mmtm) cc_final: 0.7760 (tmmt) outliers start: 13 outliers final: 10 residues processed: 91 average time/residue: 1.2488 time to fit residues: 116.4646 Evaluate side-chains 95 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.355 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 300 GLU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 739 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.159606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.132705 restraints weight = 4005.220| |-----------------------------------------------------------------------------| r_work (start): 0.3845 rms_B_bonded: 1.66 r_work: 0.3722 rms_B_bonded: 2.35 restraints_weight: 0.5000 r_work: 0.3587 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3587 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7744 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 2980 Z= 0.207 Angle : 0.444 7.240 4039 Z= 0.230 Chirality : 0.040 0.148 491 Planarity : 0.002 0.029 493 Dihedral : 7.674 56.998 397 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.23 % Allowed : 13.68 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.44), residues: 361 helix: 3.09 (0.32), residues: 229 sheet: 0.65 (0.79), residues: 42 loop : 0.27 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.011 0.001 PHE B 271 TYR 0.007 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.317 Fit side-chains REVERT: B 525 ASN cc_start: 0.7108 (OUTLIER) cc_final: 0.6854 (t160) REVERT: B 624 LYS cc_start: 0.8811 (mmtm) cc_final: 0.7805 (tmmt) REVERT: B 692 LYS cc_start: 0.8597 (mtmt) cc_final: 0.8228 (mtmt) outliers start: 13 outliers final: 8 residues processed: 93 average time/residue: 1.2328 time to fit residues: 117.3560 Evaluate side-chains 96 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 87 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 678 GLN Chi-restraints excluded: chain B residue 739 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.0060 chunk 20 optimal weight: 0.3980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 34 optimal weight: 0.5980 chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 12 optimal weight: 0.0370 chunk 14 optimal weight: 0.9980 overall best weight: 0.3874 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4192 r_free = 0.4192 target = 0.160557 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3862 r_free = 0.3862 target = 0.133671 restraints weight = 4116.008| |-----------------------------------------------------------------------------| r_work (start): 0.3856 rms_B_bonded: 1.69 r_work: 0.3737 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3599 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3599 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3442 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 2980 Z= 0.137 Angle : 0.413 7.533 4039 Z= 0.214 Chirality : 0.039 0.137 491 Planarity : 0.002 0.028 493 Dihedral : 7.502 56.755 397 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.91 % Allowed : 14.01 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.37 (0.44), residues: 361 helix: 3.26 (0.32), residues: 229 sheet: 0.59 (0.79), residues: 42 loop : 0.26 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 548 HIS 0.003 0.000 HIS B 708 PHE 0.009 0.001 PHE B 572 TYR 0.007 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.345 Fit side-chains revert: symmetry clash REVERT: B 294 GLN cc_start: 0.7339 (tt0) cc_final: 0.6701 (pm20) REVERT: B 525 ASN cc_start: 0.6969 (OUTLIER) cc_final: 0.6653 (t0) REVERT: B 624 LYS cc_start: 0.8816 (mmtm) cc_final: 0.7830 (tmmt) REVERT: B 692 LYS cc_start: 0.8603 (mtmt) cc_final: 0.8220 (mtmt) REVERT: B 737 ASP cc_start: 0.7802 (t0) cc_final: 0.7523 (t0) REVERT: B 739 LYS cc_start: 0.8565 (OUTLIER) cc_final: 0.8355 (mttp) outliers start: 12 outliers final: 5 residues processed: 92 average time/residue: 1.2290 time to fit residues: 115.8118 Evaluate side-chains 96 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 89 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 678 GLN Chi-restraints excluded: chain B residue 739 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 0.2980 chunk 14 optimal weight: 1.9990 chunk 34 optimal weight: 0.5980 chunk 28 optimal weight: 0.7980 chunk 29 optimal weight: 0.5980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN B 688 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4187 r_free = 0.4187 target = 0.160066 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3884 r_free = 0.3884 target = 0.135209 restraints weight = 4066.263| |-----------------------------------------------------------------------------| r_work (start): 0.3878 rms_B_bonded: 1.84 r_work: 0.3732 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3593 rms_B_bonded: 4.02 restraints_weight: 0.2500 r_work (final): 0.3593 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7720 moved from start: 0.3511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2980 Z= 0.179 Angle : 0.438 8.132 4039 Z= 0.224 Chirality : 0.039 0.147 491 Planarity : 0.002 0.028 493 Dihedral : 7.296 58.532 395 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 2.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.56 % Allowed : 13.36 % Favored : 82.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.35 (0.44), residues: 361 helix: 3.27 (0.32), residues: 229 sheet: 0.59 (0.79), residues: 42 loop : 0.18 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 548 HIS 0.004 0.001 HIS B 708 PHE 0.010 0.001 PHE B 654 TYR 0.007 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: B 294 GLN cc_start: 0.7340 (tt0) cc_final: 0.6660 (pm20) REVERT: B 525 ASN cc_start: 0.7068 (OUTLIER) cc_final: 0.6765 (t0) REVERT: B 624 LYS cc_start: 0.8795 (mmtm) cc_final: 0.7803 (tmmt) REVERT: B 692 LYS cc_start: 0.8599 (mtmt) cc_final: 0.8188 (mtmt) REVERT: B 718 LYS cc_start: 0.8417 (OUTLIER) cc_final: 0.8169 (ptmt) REVERT: B 737 ASP cc_start: 0.7703 (t0) cc_final: 0.7415 (t0) REVERT: B 739 LYS cc_start: 0.8549 (OUTLIER) cc_final: 0.8315 (mttp) outliers start: 14 outliers final: 8 residues processed: 92 average time/residue: 1.1961 time to fit residues: 112.7400 Evaluate side-chains 99 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 678 GLN Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 739 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 10 optimal weight: 0.0970 chunk 12 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 36 optimal weight: 0.0670 overall best weight: 0.5716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN B 688 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4188 r_free = 0.4188 target = 0.160177 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3858 r_free = 0.3858 target = 0.133340 restraints weight = 4076.706| |-----------------------------------------------------------------------------| r_work (start): 0.3853 rms_B_bonded: 1.67 r_work: 0.3732 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3597 rms_B_bonded: 4.00 restraints_weight: 0.2500 r_work (final): 0.3597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.3581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 2980 Z= 0.174 Angle : 0.440 8.676 4039 Z= 0.224 Chirality : 0.039 0.155 491 Planarity : 0.002 0.028 493 Dihedral : 7.244 58.951 395 Min Nonbonded Distance : 2.562 Molprobity Statistics. All-atom Clashscore : 2.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.56 % Allowed : 14.33 % Favored : 81.11 % 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: 3.35 (0.44), residues: 361 helix: 3.30 (0.32), residues: 229 sheet: 0.52 (0.79), residues: 42 loop : 0.14 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.011 0.001 PHE B 654 TYR 0.007 0.001 TYR B 740 ARG 0.002 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 89 time to evaluate : 0.333 Fit side-chains REVERT: B 294 GLN cc_start: 0.7293 (tt0) cc_final: 0.6681 (pm20) REVERT: B 525 ASN cc_start: 0.7015 (OUTLIER) cc_final: 0.6749 (t0) REVERT: B 624 LYS cc_start: 0.8812 (mmtm) cc_final: 0.7846 (tmmt) REVERT: B 718 LYS cc_start: 0.8450 (OUTLIER) cc_final: 0.8218 (ptmt) REVERT: B 737 ASP cc_start: 0.7709 (t0) cc_final: 0.7448 (t0) REVERT: B 739 LYS cc_start: 0.8548 (OUTLIER) cc_final: 0.8330 (mttp) outliers start: 14 outliers final: 9 residues processed: 91 average time/residue: 1.2516 time to fit residues: 116.5536 Evaluate side-chains 100 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.354 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 543 MET Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 678 GLN Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 739 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 28 optimal weight: 0.6980 chunk 13 optimal weight: 2.9990 chunk 17 optimal weight: 2.9990 chunk 8 optimal weight: 0.3980 chunk 23 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 21 optimal weight: 0.0170 chunk 12 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 26 optimal weight: 0.9990 chunk 31 optimal weight: 0.9990 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN B 688 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4193 r_free = 0.4193 target = 0.160514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3863 r_free = 0.3863 target = 0.133786 restraints weight = 4043.336| |-----------------------------------------------------------------------------| r_work (start): 0.3858 rms_B_bonded: 1.66 r_work: 0.3737 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3601 rms_B_bonded: 4.03 restraints_weight: 0.2500 r_work (final): 0.3601 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7725 moved from start: 0.3665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.019 2980 Z= 0.156 Angle : 0.461 9.032 4039 Z= 0.229 Chirality : 0.039 0.123 491 Planarity : 0.002 0.028 493 Dihedral : 7.224 59.384 395 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 2.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 4.23 % Allowed : 15.64 % Favored : 80.13 % 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: 3.46 (0.44), residues: 361 helix: 3.43 (0.32), residues: 226 sheet: 0.52 (0.79), residues: 42 loop : 0.16 (0.68), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 548 HIS 0.003 0.001 HIS B 708 PHE 0.009 0.001 PHE B 572 TYR 0.007 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 0.333 Fit side-chains REVERT: B 294 GLN cc_start: 0.7297 (tt0) cc_final: 0.6674 (pm20) REVERT: B 525 ASN cc_start: 0.6939 (OUTLIER) cc_final: 0.6723 (t0) REVERT: B 624 LYS cc_start: 0.8822 (mmtm) cc_final: 0.7843 (tmmt) REVERT: B 718 LYS cc_start: 0.8437 (OUTLIER) cc_final: 0.8210 (ptmt) REVERT: B 737 ASP cc_start: 0.7698 (t0) cc_final: 0.7447 (t0) REVERT: B 739 LYS cc_start: 0.8550 (OUTLIER) cc_final: 0.8318 (mttp) outliers start: 13 outliers final: 10 residues processed: 92 average time/residue: 1.2022 time to fit residues: 113.3210 Evaluate side-chains 101 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 88 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 525 ASN Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 560 ILE Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 678 GLN Chi-restraints excluded: chain B residue 690 VAL Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 739 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 27 optimal weight: 0.4980 chunk 6 optimal weight: 0.9990 chunk 1 optimal weight: 10.0000 chunk 21 optimal weight: 0.0170 chunk 7 optimal weight: 0.9980 chunk 3 optimal weight: 0.0270 chunk 25 optimal weight: 0.4980 chunk 22 optimal weight: 2.9990 chunk 8 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 0.9990 overall best weight: 0.3476 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 531 GLN B 648 GLN B 688 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4201 r_free = 0.4201 target = 0.161248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3872 r_free = 0.3872 target = 0.134504 restraints weight = 4043.437| |-----------------------------------------------------------------------------| r_work (start): 0.3870 rms_B_bonded: 1.67 r_work: 0.3750 rms_B_bonded: 2.36 restraints_weight: 0.5000 r_work: 0.3614 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3614 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.3770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 2980 Z= 0.138 Angle : 0.472 9.841 4039 Z= 0.233 Chirality : 0.039 0.132 491 Planarity : 0.002 0.027 493 Dihedral : 7.206 59.529 395 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.91 % Allowed : 16.29 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.44), residues: 361 helix: 3.45 (0.32), residues: 226 sheet: 0.51 (0.79), residues: 42 loop : 0.19 (0.68), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 548 HIS 0.002 0.000 HIS B 708 PHE 0.010 0.001 PHE B 572 TYR 0.007 0.001 TYR B 740 ARG 0.001 0.000 ARG B 720 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 722 Ramachandran restraints generated. 361 Oldfield, 0 Emsley, 361 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 90 time to evaluate : 0.338 Fit side-chains REVERT: B 294 GLN cc_start: 0.7260 (tt0) cc_final: 0.6640 (pm20) REVERT: B 624 LYS cc_start: 0.8819 (mmtm) cc_final: 0.7843 (tmmt) REVERT: B 718 LYS cc_start: 0.8415 (OUTLIER) cc_final: 0.8182 (ptmt) REVERT: B 737 ASP cc_start: 0.7704 (t0) cc_final: 0.7452 (t0) REVERT: B 739 LYS cc_start: 0.8541 (OUTLIER) cc_final: 0.8313 (mttp) outliers start: 12 outliers final: 8 residues processed: 93 average time/residue: 1.1529 time to fit residues: 109.9796 Evaluate side-chains 98 residues out of total 344 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 266 THR Chi-restraints excluded: chain B residue 317 LEU Chi-restraints excluded: chain B residue 549 LEU Chi-restraints excluded: chain B residue 562 LEU Chi-restraints excluded: chain B residue 563 LEU Chi-restraints excluded: chain B residue 579 LYS Chi-restraints excluded: chain B residue 662 VAL Chi-restraints excluded: chain B residue 678 GLN Chi-restraints excluded: chain B residue 718 LYS Chi-restraints excluded: chain B residue 739 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 7.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 22 optimal weight: 0.9990 chunk 32 optimal weight: 0.9980 chunk 5 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 525 ASN B 531 GLN B 648 GLN B 688 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4173 r_free = 0.4173 target = 0.159012 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3840 r_free = 0.3840 target = 0.132123 restraints weight = 3975.435| |-----------------------------------------------------------------------------| r_work (start): 0.3836 rms_B_bonded: 1.67 r_work: 0.3713 rms_B_bonded: 2.34 restraints_weight: 0.5000 r_work: 0.3576 rms_B_bonded: 3.98 restraints_weight: 0.2500 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 2980 Z= 0.248 Angle : 0.534 10.199 4039 Z= 0.267 Chirality : 0.041 0.191 491 Planarity : 0.003 0.041 493 Dihedral : 7.362 57.703 395 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.39 % Favored : 98.61 % Rotamer: Outliers : 3.26 % Allowed : 17.26 % Favored : 79.48 % 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: 3.24 (0.44), residues: 361 helix: 3.19 (0.32), residues: 229 sheet: 0.49 (0.79), residues: 42 loop : 0.13 (0.68), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 316 HIS 0.004 0.001 HIS B 708 PHE 0.013 0.002 PHE B 271 TYR 0.008 0.001 TYR B 740 ARG 0.002 0.000 ARG B 296 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4613.45 seconds wall clock time: 81 minutes 38.59 seconds (4898.59 seconds total)