Starting phenix.real_space_refine on Tue Mar 3 13:18:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7mlz_23914/03_2026/7mlz_23914.cif Found real_map, /net/cci-nas-00/data/ceres_data/7mlz_23914/03_2026/7mlz_23914.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.71 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7mlz_23914/03_2026/7mlz_23914.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7mlz_23914/03_2026/7mlz_23914.map" model { file = "/net/cci-nas-00/data/ceres_data/7mlz_23914/03_2026/7mlz_23914.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7mlz_23914/03_2026/7mlz_23914.cif" } resolution = 3.71 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.006 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 22 5.16 5 C 3073 2.51 5 N 809 2.21 5 O 960 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4864 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "H" Number of atoms: 1611 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 215, 1611 Classifications: {'peptide': 215} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 202} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "L" Number of atoms: 1641 Number of conformers: 1 Conformer: "A" Number of residues, atoms: 213, 1641 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "B" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Time building chain proxies: 1.16, per 1000 atoms: 0.24 Number of scatterers: 4864 At special positions: 0 Unit cell: (86.427, 61.983, 138.807, 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 22 16.00 O 960 8.00 N 809 7.00 C 3073 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.05 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS H 97 " - pdb=" SG CYS H 100B" distance=2.04 Simple disulfide: pdb=" SG CYS H 140 " - pdb=" SG CYS H 196 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG CYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied ALPHA1-3 " BMA B 3 " - " MAN B 4 " ALPHA1-6 " BMA B 3 " - " MAN B 5 " BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG B 1 " - " ASN A 343 " Time building additional restraints: 0.40 Conformation dependent library (CDL) restraints added in 207.5 milliseconds 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1152 Finding SS restraints... Secondary structure from input PDB file: 5 helices and 14 sheets defined 5.0% alpha, 18.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 4.049A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 removed outlier: 3.706A pdb=" N TYR A 369 " --> pdb=" O TYR A 365 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.674A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) removed outlier: 3.648A pdb=" N GLN A 409 " --> pdb=" O GLU A 406 " (cutoff:3.500A) Processing helix chain 'H' and resid 73 through 77 removed outlier: 3.968A pdb=" N THR H 77 " --> pdb=" O SER H 74 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 126 removed outlier: 3.598A pdb=" N LEU L 125 " --> pdb=" O ASP L 122 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.689A pdb=" N ILE A 402 " --> pdb=" O TYR A 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 356 through 358 Processing sheet with id=AA3, first strand: chain 'H' and resid 4 through 6 removed outlier: 3.599A pdb=" N VAL H 5 " --> pdb=" O LYS H 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.896A pdb=" N LYS H 12 " --> pdb=" O THR H 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 18 through 19 Processing sheet with id=AA6, first strand: chain 'H' and resid 33 through 38 removed outlier: 6.146A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.827A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N VAL H 52 " --> pdb=" O ASN H 56 " (cutoff:3.500A) removed outlier: 3.826A pdb=" N ASN H 56 " --> pdb=" O VAL H 52 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'H' and resid 93 through 94 Processing sheet with id=AA8, first strand: chain 'H' and resid 120 through 124 removed outlier: 4.262A pdb=" N GLY H 139 " --> pdb=" O LEU H 124 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N TYR H 176 " --> pdb=" O ASP H 144 " (cutoff:3.500A) removed outlier: 6.269A pdb=" N SER H 177 " --> pdb=" O ALA H 168 " (cutoff:3.500A) removed outlier: 4.326A pdb=" N ALA H 168 " --> pdb=" O SER H 177 " (cutoff:3.500A) removed outlier: 4.235A pdb=" N SER H 179 " --> pdb=" O PHE H 166 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 198 through 200 removed outlier: 3.504A pdb=" N THR H 205 " --> pdb=" O HIS H 200 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 10 through 12 removed outlier: 5.825A pdb=" N LEU L 11 " --> pdb=" O GLU L 105 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB1 Processing sheet with id=AB2, first strand: chain 'L' and resid 20 through 24 Processing sheet with id=AB3, first strand: chain 'L' and resid 33 through 37 removed outlier: 4.059A pdb=" N ALA L 34 " --> pdb=" O GLN L 89 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N TYR L 87 " --> pdb=" O TYR L 36 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'L' and resid 117 through 118 removed outlier: 3.538A pdb=" N THR L 178 " --> pdb=" O GLN L 160 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N GLN L 160 " --> pdb=" O THR L 178 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'L' and resid 146 through 147 removed outlier: 3.520A pdb=" N GLU L 195 " --> pdb=" O GLN L 147 " (cutoff:3.500A) 74 hydrogen bonds defined for protein. 171 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: 0.64 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.35: 1544 1.35 - 1.48: 1377 1.48 - 1.60: 2037 1.60 - 1.73: 0 1.73 - 1.85: 26 Bond restraints: 4984 Sorted by residual: bond pdb=" C1 NAG B 1 " pdb=" O5 NAG B 1 " ideal model delta sigma weight residual 1.406 1.453 -0.047 2.00e-02 2.50e+03 5.46e+00 bond pdb=" C1 MAN B 4 " pdb=" C2 MAN B 4 " ideal model delta sigma weight residual 1.526 1.569 -0.043 2.00e-02 2.50e+03 4.73e+00 bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.560 -0.041 2.00e-02 2.50e+03 4.30e+00 bond pdb=" C1 MAN B 4 " pdb=" O5 MAN B 4 " ideal model delta sigma weight residual 1.399 1.432 -0.033 2.00e-02 2.50e+03 2.72e+00 bond pdb=" C GLN A 498 " pdb=" N PRO A 499 " ideal model delta sigma weight residual 1.334 1.346 -0.013 8.40e-03 1.42e+04 2.34e+00 ... (remaining 4979 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 6440 1.62 - 3.25: 262 3.25 - 4.87: 59 4.87 - 6.49: 15 6.49 - 8.12: 6 Bond angle restraints: 6782 Sorted by residual: angle pdb=" C THR H 191 " pdb=" N GLN H 192 " pdb=" CA GLN H 192 " ideal model delta sigma weight residual 121.54 128.49 -6.95 1.91e+00 2.74e-01 1.33e+01 angle pdb=" CA CYS A 379 " pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " ideal model delta sigma weight residual 114.40 122.52 -8.12 2.30e+00 1.89e-01 1.25e+01 angle pdb=" C PHE A 347 " pdb=" N ALA A 348 " pdb=" CA ALA A 348 " ideal model delta sigma weight residual 121.54 128.07 -6.53 1.91e+00 2.74e-01 1.17e+01 angle pdb=" C SER L 30 " pdb=" N SER L 31 " pdb=" CA SER L 31 " ideal model delta sigma weight residual 121.54 127.13 -5.59 1.91e+00 2.74e-01 8.56e+00 angle pdb=" CA GLY H 55 " pdb=" C GLY H 55 " pdb=" N ASN H 56 " ideal model delta sigma weight residual 117.06 114.03 3.03 1.08e+00 8.57e-01 7.89e+00 ... (remaining 6777 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.98: 2835 22.98 - 45.97: 165 45.97 - 68.95: 14 68.95 - 91.94: 12 91.94 - 114.92: 4 Dihedral angle restraints: 3030 sinusoidal: 1225 harmonic: 1805 Sorted by residual: dihedral pdb=" CB CYS L 134 " pdb=" SG CYS L 134 " pdb=" SG CYS L 194 " pdb=" CB CYS L 194 " ideal model delta sinusoidal sigma weight residual 93.00 179.47 -86.47 1 1.00e+01 1.00e-02 9.01e+01 dihedral pdb=" CB CYS A 336 " pdb=" SG CYS A 336 " pdb=" SG CYS A 361 " pdb=" CB CYS A 361 " ideal model delta sinusoidal sigma weight residual 93.00 15.07 77.93 1 1.00e+01 1.00e-02 7.59e+01 dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 32.88 60.12 1 1.00e+01 1.00e-02 4.82e+01 ... (remaining 3027 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.051: 568 0.051 - 0.101: 154 0.101 - 0.152: 35 0.152 - 0.203: 4 0.203 - 0.254: 2 Chirality restraints: 763 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.53 0.25 2.00e-01 2.50e+01 1.61e+00 chirality pdb=" CB ILE L 48 " pdb=" CA ILE L 48 " pdb=" CG1 ILE L 48 " pdb=" CG2 ILE L 48 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.08e+00 chirality pdb=" CA LYS H 201 " pdb=" N LYS H 201 " pdb=" C LYS H 201 " pdb=" CB LYS H 201 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.34e-01 ... (remaining 760 not shown) Planarity restraints: 868 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA L 112 " -0.034 5.00e-02 4.00e+02 5.16e-02 4.26e+00 pdb=" N PRO L 113 " 0.089 5.00e-02 4.00e+02 pdb=" CA PRO L 113 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO L 113 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 429 " 0.014 2.00e-02 2.50e+03 1.53e-02 4.12e+00 pdb=" CG PHE A 429 " -0.036 2.00e-02 2.50e+03 pdb=" CD1 PHE A 429 " 0.006 2.00e-02 2.50e+03 pdb=" CD2 PHE A 429 " 0.012 2.00e-02 2.50e+03 pdb=" CE1 PHE A 429 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 PHE A 429 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE A 429 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA A 411 " -0.031 5.00e-02 4.00e+02 4.75e-02 3.62e+00 pdb=" N PRO A 412 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO A 412 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 412 " -0.027 5.00e-02 4.00e+02 ... (remaining 865 not shown) Histogram of nonbonded interaction distances: 2.15 - 2.70: 212 2.70 - 3.25: 5009 3.25 - 3.80: 7178 3.80 - 4.35: 9034 4.35 - 4.90: 14971 Nonbonded interactions: 36404 Sorted by model distance: nonbonded pdb=" OG1 THR H 28 " pdb=" O CYS H 97 " model vdw 2.150 3.040 nonbonded pdb=" OG1 THR L 20 " pdb=" O LEU L 73 " model vdw 2.196 3.040 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.201 3.040 nonbonded pdb=" O ARG L 61 " pdb=" OG SER L 76 " model vdw 2.204 3.040 nonbonded pdb=" NH2 ARG A 357 " pdb=" OH TYR A 396 " model vdw 2.236 3.120 ... (remaining 36399 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 12.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 5.970 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6220 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4998 Z= 0.191 Angle : 0.843 11.298 6815 Z= 0.426 Chirality : 0.050 0.254 763 Planarity : 0.005 0.052 867 Dihedral : 14.730 114.921 1851 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 18.02 Ramachandran Plot: Outliers : 0.16 % Allowed : 17.37 % Favored : 82.47 % Rotamer: Outliers : 0.00 % Allowed : 0.37 % Favored : 99.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.08 (0.31), residues: 616 helix: -4.58 (0.49), residues: 20 sheet: -2.30 (0.39), residues: 167 loop : -2.99 (0.28), residues: 429 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG H 38 TYR 0.029 0.002 TYR L 49 PHE 0.036 0.002 PHE A 429 TRP 0.022 0.002 TRP H 47 HIS 0.004 0.001 HIS H 200 Details of bonding type rmsd covalent geometry : bond 0.00407 ( 4984) covalent geometry : angle 0.82130 ( 6782) SS BOND : bond 0.00691 ( 9) SS BOND : angle 1.84933 ( 18) hydrogen bonds : bond 0.28352 ( 68) hydrogen bonds : angle 12.41165 ( 171) link_ALPHA1-3 : bond 0.00684 ( 1) link_ALPHA1-3 : angle 1.08998 ( 3) link_ALPHA1-6 : bond 0.00424 ( 1) link_ALPHA1-6 : angle 1.56509 ( 3) link_BETA1-4 : bond 0.00838 ( 2) link_BETA1-4 : angle 2.22433 ( 6) link_NAG-ASN : bond 0.00775 ( 1) link_NAG-ASN : angle 7.33545 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 89 time to evaluate : 0.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8718 (mp) cc_final: 0.8491 (mm) REVERT: H 72 ASP cc_start: 0.7392 (t0) cc_final: 0.6045 (t0) outliers start: 0 outliers final: 0 residues processed: 89 average time/residue: 0.0984 time to fit residues: 10.7481 Evaluate side-chains 69 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 69 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.2980 chunk 24 optimal weight: 0.7980 chunk 48 optimal weight: 0.1980 chunk 56 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 6 GLN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 138 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.094657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.086087 restraints weight = 23021.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.087976 restraints weight = 14241.013| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.089245 restraints weight = 9692.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3988 r_free = 0.3988 target = 0.090130 restraints weight = 7093.220| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.090764 restraints weight = 5484.563| |-----------------------------------------------------------------------------| r_work (final): 0.3999 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3999 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 1.00 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3999 r_free = 0.3999 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3999 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6399 moved from start: 0.1345 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 4998 Z= 0.154 Angle : 0.790 11.449 6815 Z= 0.395 Chirality : 0.049 0.161 763 Planarity : 0.005 0.050 867 Dihedral : 11.291 91.426 777 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.10 % Favored : 84.74 % Rotamer: Outliers : 1.12 % Allowed : 11.96 % Favored : 86.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.21 (0.30), residues: 616 helix: -4.17 (0.48), residues: 26 sheet: -2.28 (0.39), residues: 168 loop : -3.13 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.013 0.002 TYR H 96 PHE 0.025 0.002 PHE H 27 TRP 0.021 0.002 TRP L 35 HIS 0.004 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00343 ( 4984) covalent geometry : angle 0.76585 ( 6782) SS BOND : bond 0.00597 ( 9) SS BOND : angle 1.59724 ( 18) hydrogen bonds : bond 0.05247 ( 68) hydrogen bonds : angle 8.77340 ( 171) link_ALPHA1-3 : bond 0.01296 ( 1) link_ALPHA1-3 : angle 1.85513 ( 3) link_ALPHA1-6 : bond 0.00780 ( 1) link_ALPHA1-6 : angle 1.52233 ( 3) link_BETA1-4 : bond 0.00871 ( 2) link_BETA1-4 : angle 2.57540 ( 6) link_NAG-ASN : bond 0.00618 ( 1) link_NAG-ASN : angle 7.63723 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 78 time to evaluate : 0.193 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8801 (mp) cc_final: 0.8556 (mm) REVERT: H 72 ASP cc_start: 0.8183 (t0) cc_final: 0.7664 (t0) outliers start: 6 outliers final: 4 residues processed: 80 average time/residue: 0.0859 time to fit residues: 8.7362 Evaluate side-chains 75 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 71 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 31 optimal weight: 0.3980 chunk 7 optimal weight: 0.4980 chunk 30 optimal weight: 0.4980 chunk 59 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 11 optimal weight: 0.3980 chunk 53 optimal weight: 2.9990 chunk 60 optimal weight: 1.9990 chunk 3 optimal weight: 0.3980 chunk 33 optimal weight: 1.9990 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.095075 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3921 r_free = 0.3921 target = 0.086637 restraints weight = 23159.017| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.088475 restraints weight = 14308.846| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3982 r_free = 0.3982 target = 0.089718 restraints weight = 9767.879| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.090579 restraints weight = 7172.576| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.091201 restraints weight = 5548.375| |-----------------------------------------------------------------------------| r_work (final): 0.4011 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4011 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.08 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4011 r_free = 0.4011 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4011 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6352 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4998 Z= 0.132 Angle : 0.758 11.781 6815 Z= 0.377 Chirality : 0.048 0.179 763 Planarity : 0.005 0.047 867 Dihedral : 10.098 77.900 777 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 13.41 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.58 % Favored : 84.25 % Rotamer: Outliers : 0.75 % Allowed : 15.51 % Favored : 83.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.26 (0.30), residues: 616 helix: -4.04 (0.52), residues: 26 sheet: -2.29 (0.40), residues: 158 loop : -3.19 (0.26), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.013 0.001 TYR H 79 PHE 0.027 0.002 PHE H 27 TRP 0.021 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00287 ( 4984) covalent geometry : angle 0.73438 ( 6782) SS BOND : bond 0.00588 ( 9) SS BOND : angle 0.98636 ( 18) hydrogen bonds : bond 0.04047 ( 68) hydrogen bonds : angle 7.92995 ( 171) link_ALPHA1-3 : bond 0.01390 ( 1) link_ALPHA1-3 : angle 1.35941 ( 3) link_ALPHA1-6 : bond 0.00923 ( 1) link_ALPHA1-6 : angle 1.45365 ( 3) link_BETA1-4 : bond 0.00834 ( 2) link_BETA1-4 : angle 2.47284 ( 6) link_NAG-ASN : bond 0.00477 ( 1) link_NAG-ASN : angle 8.01506 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 81 time to evaluate : 0.184 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8855 (mp) cc_final: 0.8587 (mm) REVERT: H 72 ASP cc_start: 0.8207 (t0) cc_final: 0.7940 (t0) outliers start: 4 outliers final: 4 residues processed: 83 average time/residue: 0.0906 time to fit residues: 9.4559 Evaluate side-chains 76 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 72 time to evaluate : 0.186 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 54 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 52 optimal weight: 0.0980 chunk 48 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4071 r_free = 0.4071 target = 0.094266 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.085883 restraints weight = 22852.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3943 r_free = 0.3943 target = 0.087708 restraints weight = 14164.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3967 r_free = 0.3967 target = 0.088932 restraints weight = 9681.120| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.089786 restraints weight = 7124.052| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.090406 restraints weight = 5517.725| |-----------------------------------------------------------------------------| r_work (final): 0.3995 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3995 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.05 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3995 r_free = 0.3995 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3995 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6397 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4998 Z= 0.144 Angle : 0.742 11.812 6815 Z= 0.372 Chirality : 0.048 0.159 763 Planarity : 0.005 0.047 867 Dihedral : 8.863 62.368 777 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.40 % Favored : 83.44 % Rotamer: Outliers : 2.62 % Allowed : 17.94 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.29 (0.30), residues: 616 helix: -4.09 (0.47), residues: 27 sheet: -2.34 (0.38), residues: 170 loop : -3.19 (0.26), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.019 0.001 TYR H 96 PHE 0.029 0.002 PHE H 27 TRP 0.010 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00322 ( 4984) covalent geometry : angle 0.71810 ( 6782) SS BOND : bond 0.00358 ( 9) SS BOND : angle 1.04140 ( 18) hydrogen bonds : bond 0.03779 ( 68) hydrogen bonds : angle 7.50107 ( 171) link_ALPHA1-3 : bond 0.01403 ( 1) link_ALPHA1-3 : angle 1.78855 ( 3) link_ALPHA1-6 : bond 0.00835 ( 1) link_ALPHA1-6 : angle 1.58277 ( 3) link_BETA1-4 : bond 0.00888 ( 2) link_BETA1-4 : angle 2.25501 ( 6) link_NAG-ASN : bond 0.00781 ( 1) link_NAG-ASN : angle 7.87075 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 0.186 Fit side-chains REVERT: A 402 ILE cc_start: 0.8857 (mp) cc_final: 0.8591 (mm) REVERT: H 72 ASP cc_start: 0.8110 (t0) cc_final: 0.7888 (t0) REVERT: H 100 PHE cc_start: 0.7246 (OUTLIER) cc_final: 0.6450 (t80) REVERT: H 117 LYS cc_start: 0.7373 (pptt) cc_final: 0.6401 (pptt) REVERT: H 144 ASP cc_start: 0.8458 (OUTLIER) cc_final: 0.7116 (t0) outliers start: 14 outliers final: 8 residues processed: 88 average time/residue: 0.0713 time to fit residues: 8.0977 Evaluate side-chains 85 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 75 time to evaluate : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 60 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 52 optimal weight: 2.9990 chunk 9 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 42 optimal weight: 2.9990 chunk 19 optimal weight: 0.0980 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.0060 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 158 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4074 r_free = 0.4074 target = 0.094261 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3907 r_free = 0.3907 target = 0.085860 restraints weight = 23098.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.087688 restraints weight = 14324.460| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.088938 restraints weight = 9815.194| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.089777 restraints weight = 7187.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.090418 restraints weight = 5588.433| |-----------------------------------------------------------------------------| r_work (final): 0.3997 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3997 r_free = 0.3997 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6385 moved from start: 0.2179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4998 Z= 0.142 Angle : 0.772 11.710 6815 Z= 0.385 Chirality : 0.049 0.256 763 Planarity : 0.005 0.049 867 Dihedral : 7.985 59.722 777 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 13.74 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.42 % Favored : 84.42 % Rotamer: Outliers : 2.80 % Allowed : 20.00 % Favored : 77.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.30 (0.29), residues: 616 helix: -3.93 (0.53), residues: 27 sheet: -2.48 (0.39), residues: 164 loop : -3.14 (0.26), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.036 0.002 TYR L 49 PHE 0.032 0.002 PHE H 27 TRP 0.023 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00319 ( 4984) covalent geometry : angle 0.74596 ( 6782) SS BOND : bond 0.00476 ( 9) SS BOND : angle 1.81835 ( 18) hydrogen bonds : bond 0.03511 ( 68) hydrogen bonds : angle 7.59820 ( 171) link_ALPHA1-3 : bond 0.01311 ( 1) link_ALPHA1-3 : angle 1.77236 ( 3) link_ALPHA1-6 : bond 0.00960 ( 1) link_ALPHA1-6 : angle 1.85327 ( 3) link_BETA1-4 : bond 0.00822 ( 2) link_BETA1-4 : angle 2.01565 ( 6) link_NAG-ASN : bond 0.00726 ( 1) link_NAG-ASN : angle 7.90157 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 81 time to evaluate : 0.204 Fit side-chains REVERT: A 402 ILE cc_start: 0.8850 (mp) cc_final: 0.8588 (mm) REVERT: H 72 ASP cc_start: 0.8120 (t0) cc_final: 0.7878 (t0) REVERT: H 100 PHE cc_start: 0.7134 (OUTLIER) cc_final: 0.6911 (t80) REVERT: H 117 LYS cc_start: 0.7326 (pptt) cc_final: 0.6286 (pptt) REVERT: H 144 ASP cc_start: 0.8459 (OUTLIER) cc_final: 0.7137 (t0) outliers start: 15 outliers final: 8 residues processed: 92 average time/residue: 0.0892 time to fit residues: 10.3698 Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 6.9990 chunk 35 optimal weight: 2.9990 chunk 20 optimal weight: 0.0040 chunk 37 optimal weight: 0.0670 chunk 0 optimal weight: 2.9990 chunk 52 optimal weight: 0.0040 chunk 44 optimal weight: 4.9990 chunk 30 optimal weight: 0.6980 chunk 56 optimal weight: 0.3980 chunk 25 optimal weight: 0.0670 chunk 39 optimal weight: 2.9990 overall best weight: 0.1080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 58 ASN ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.096004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.087656 restraints weight = 23246.806| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.089499 restraints weight = 14295.336| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4009 r_free = 0.4009 target = 0.090751 restraints weight = 9739.153| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4026 r_free = 0.4026 target = 0.091624 restraints weight = 7085.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4038 r_free = 0.4038 target = 0.092237 restraints weight = 5455.199| |-----------------------------------------------------------------------------| r_work (final): 0.4036 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4036 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4036 r_free = 0.4036 target_work(ls_wunit_k1) = 0.092 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4036 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6281 moved from start: 0.2527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4998 Z= 0.126 Angle : 0.770 11.921 6815 Z= 0.382 Chirality : 0.048 0.193 763 Planarity : 0.005 0.047 867 Dihedral : 7.085 58.708 777 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 12.48 Ramachandran Plot: Outliers : 0.16 % Allowed : 12.50 % Favored : 87.34 % Rotamer: Outliers : 2.99 % Allowed : 20.00 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.23 (0.30), residues: 616 helix: -4.10 (0.50), residues: 27 sheet: -2.41 (0.39), residues: 166 loop : -3.08 (0.26), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG H 71 TYR 0.017 0.001 TYR L 140 PHE 0.033 0.002 PHE H 27 TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00276 ( 4984) covalent geometry : angle 0.74485 ( 6782) SS BOND : bond 0.00547 ( 9) SS BOND : angle 1.53305 ( 18) hydrogen bonds : bond 0.03271 ( 68) hydrogen bonds : angle 7.22075 ( 171) link_ALPHA1-3 : bond 0.01320 ( 1) link_ALPHA1-3 : angle 1.60404 ( 3) link_ALPHA1-6 : bond 0.00972 ( 1) link_ALPHA1-6 : angle 2.09059 ( 3) link_BETA1-4 : bond 0.00841 ( 2) link_BETA1-4 : angle 1.62468 ( 6) link_NAG-ASN : bond 0.00536 ( 1) link_NAG-ASN : angle 8.16703 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 79 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8828 (mp) cc_final: 0.8570 (mm) REVERT: H 72 ASP cc_start: 0.8101 (t0) cc_final: 0.7868 (t0) REVERT: H 117 LYS cc_start: 0.7135 (pptt) cc_final: 0.6012 (pptt) REVERT: H 144 ASP cc_start: 0.8528 (OUTLIER) cc_final: 0.7497 (t0) outliers start: 16 outliers final: 7 residues processed: 90 average time/residue: 0.0828 time to fit residues: 9.3830 Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 110 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 0 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 37 optimal weight: 0.1980 chunk 42 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 49 optimal weight: 0.5980 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4073 r_free = 0.4073 target = 0.094055 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3906 r_free = 0.3906 target = 0.085712 restraints weight = 23251.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3944 r_free = 0.3944 target = 0.087572 restraints weight = 14314.543| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.088814 restraints weight = 9735.698| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3984 r_free = 0.3984 target = 0.089636 restraints weight = 7121.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.090275 restraints weight = 5537.995| |-----------------------------------------------------------------------------| r_work (final): 0.3996 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3996 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3996 r_free = 0.3996 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3996 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6377 moved from start: 0.2582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 4998 Z= 0.153 Angle : 0.775 11.981 6815 Z= 0.386 Chirality : 0.047 0.155 763 Planarity : 0.005 0.047 867 Dihedral : 6.692 58.246 777 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 13.32 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.75 % Favored : 84.09 % Rotamer: Outliers : 2.43 % Allowed : 20.75 % Favored : 76.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.22 (0.30), residues: 616 helix: -3.85 (0.55), residues: 27 sheet: -2.27 (0.38), residues: 170 loop : -3.17 (0.27), residues: 419 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 71 TYR 0.019 0.001 TYR H 96 PHE 0.031 0.002 PHE H 27 TRP 0.028 0.002 TRP H 47 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00345 ( 4984) covalent geometry : angle 0.75105 ( 6782) SS BOND : bond 0.00443 ( 9) SS BOND : angle 1.30203 ( 18) hydrogen bonds : bond 0.03534 ( 68) hydrogen bonds : angle 7.00305 ( 171) link_ALPHA1-3 : bond 0.01233 ( 1) link_ALPHA1-3 : angle 2.02177 ( 3) link_ALPHA1-6 : bond 0.01025 ( 1) link_ALPHA1-6 : angle 2.17600 ( 3) link_BETA1-4 : bond 0.00808 ( 2) link_BETA1-4 : angle 1.51529 ( 6) link_NAG-ASN : bond 0.00597 ( 1) link_NAG-ASN : angle 8.16172 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 76 time to evaluate : 0.188 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8872 (mp) cc_final: 0.8598 (mm) REVERT: H 72 ASP cc_start: 0.8126 (t0) cc_final: 0.7864 (t0) REVERT: H 117 LYS cc_start: 0.7266 (pptt) cc_final: 0.6190 (pptt) REVERT: H 144 ASP cc_start: 0.8471 (OUTLIER) cc_final: 0.7292 (t0) REVERT: L 18 ARG cc_start: 0.7048 (tpm170) cc_final: 0.6848 (tpm170) outliers start: 13 outliers final: 7 residues processed: 85 average time/residue: 0.0820 time to fit residues: 8.8687 Evaluate side-chains 83 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 0.181 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 49 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 54 optimal weight: 0.0770 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 46 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 40 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 overall best weight: 0.6138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4078 r_free = 0.4078 target = 0.094303 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3912 r_free = 0.3912 target = 0.085943 restraints weight = 23291.146| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.087799 restraints weight = 14370.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3974 r_free = 0.3974 target = 0.089046 restraints weight = 9786.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.089918 restraints weight = 7156.739| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 38)----------------| | r_work = 0.4003 r_free = 0.4003 target = 0.090541 restraints weight = 5533.086| |-----------------------------------------------------------------------------| r_work (final): 0.4002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4002 r_free = 0.4002 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4002 r_free = 0.4002 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4002 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6370 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 4998 Z= 0.145 Angle : 0.773 11.756 6815 Z= 0.386 Chirality : 0.048 0.154 763 Planarity : 0.005 0.048 867 Dihedral : 6.545 58.699 777 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 13.00 Ramachandran Plot: Outliers : 0.16 % Allowed : 15.75 % Favored : 84.09 % Rotamer: Outliers : 2.62 % Allowed : 21.31 % Favored : 76.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.18 (0.30), residues: 616 helix: -3.58 (0.62), residues: 27 sheet: -2.29 (0.38), residues: 172 loop : -3.14 (0.27), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 71 TYR 0.018 0.001 TYR L 140 PHE 0.037 0.002 PHE H 27 TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS L 189 Details of bonding type rmsd covalent geometry : bond 0.00333 ( 4984) covalent geometry : angle 0.74915 ( 6782) SS BOND : bond 0.00500 ( 9) SS BOND : angle 1.39352 ( 18) hydrogen bonds : bond 0.03386 ( 68) hydrogen bonds : angle 6.85743 ( 171) link_ALPHA1-3 : bond 0.01265 ( 1) link_ALPHA1-3 : angle 1.91249 ( 3) link_ALPHA1-6 : bond 0.00947 ( 1) link_ALPHA1-6 : angle 2.25022 ( 3) link_BETA1-4 : bond 0.00771 ( 2) link_BETA1-4 : angle 1.43039 ( 6) link_NAG-ASN : bond 0.00560 ( 1) link_NAG-ASN : angle 8.00228 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 77 time to evaluate : 0.140 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8868 (mp) cc_final: 0.8594 (mm) REVERT: H 72 ASP cc_start: 0.8162 (t0) cc_final: 0.7882 (t0) REVERT: H 117 LYS cc_start: 0.7281 (pptt) cc_final: 0.6232 (pptt) REVERT: H 144 ASP cc_start: 0.8438 (OUTLIER) cc_final: 0.7248 (t0) REVERT: L 175 LEU cc_start: 0.7738 (OUTLIER) cc_final: 0.7524 (mt) outliers start: 14 outliers final: 7 residues processed: 88 average time/residue: 0.0813 time to fit residues: 9.1819 Evaluate side-chains 80 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 71 time to evaluate : 0.184 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 1.9990 chunk 2 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 21 optimal weight: 4.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4061 r_free = 0.4061 target = 0.093527 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3897 r_free = 0.3897 target = 0.085296 restraints weight = 22980.793| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3934 r_free = 0.3934 target = 0.087103 restraints weight = 14167.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3959 r_free = 0.3959 target = 0.088339 restraints weight = 9655.311| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.089197 restraints weight = 7048.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.089800 restraints weight = 5455.253| |-----------------------------------------------------------------------------| r_work (final): 0.3987 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3987 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3987 r_free = 0.3987 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3987 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6410 moved from start: 0.2785 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4998 Z= 0.162 Angle : 0.791 11.789 6815 Z= 0.396 Chirality : 0.049 0.302 763 Planarity : 0.005 0.047 867 Dihedral : 6.491 57.102 777 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.56 % Favored : 83.28 % Rotamer: Outliers : 2.24 % Allowed : 21.12 % Favored : 76.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.16 (0.30), residues: 616 helix: -3.35 (0.70), residues: 26 sheet: -2.30 (0.39), residues: 172 loop : -3.13 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 38 TYR 0.020 0.002 TYR L 140 PHE 0.035 0.002 PHE H 27 TRP 0.016 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00370 ( 4984) covalent geometry : angle 0.76720 ( 6782) SS BOND : bond 0.00454 ( 9) SS BOND : angle 1.51359 ( 18) hydrogen bonds : bond 0.03538 ( 68) hydrogen bonds : angle 6.87476 ( 171) link_ALPHA1-3 : bond 0.01201 ( 1) link_ALPHA1-3 : angle 1.98880 ( 3) link_ALPHA1-6 : bond 0.01010 ( 1) link_ALPHA1-6 : angle 2.19182 ( 3) link_BETA1-4 : bond 0.00739 ( 2) link_BETA1-4 : angle 1.43544 ( 6) link_NAG-ASN : bond 0.00578 ( 1) link_NAG-ASN : angle 7.97503 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 0.195 Fit side-chains revert: symmetry clash REVERT: A 402 ILE cc_start: 0.8884 (mp) cc_final: 0.8672 (mm) REVERT: H 72 ASP cc_start: 0.8109 (t0) cc_final: 0.7820 (t0) REVERT: H 100 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6919 (t80) REVERT: H 117 LYS cc_start: 0.7331 (pptt) cc_final: 0.6200 (pptt) REVERT: H 144 ASP cc_start: 0.8412 (OUTLIER) cc_final: 0.7239 (t0) REVERT: L 175 LEU cc_start: 0.7772 (OUTLIER) cc_final: 0.7532 (mt) outliers start: 12 outliers final: 9 residues processed: 84 average time/residue: 0.0841 time to fit residues: 8.9962 Evaluate side-chains 84 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 72 time to evaluate : 0.182 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 133 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 3 optimal weight: 0.9980 chunk 44 optimal weight: 4.9990 chunk 54 optimal weight: 0.1980 chunk 43 optimal weight: 0.5980 chunk 46 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 55 optimal weight: 0.0040 chunk 48 optimal weight: 0.0470 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 overall best weight: 0.3290 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.094849 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3925 r_free = 0.3925 target = 0.086519 restraints weight = 23159.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3962 r_free = 0.3962 target = 0.088350 restraints weight = 14253.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.089595 restraints weight = 9730.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4002 r_free = 0.4002 target = 0.090446 restraints weight = 7121.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.091074 restraints weight = 5524.340| |-----------------------------------------------------------------------------| r_work (final): 0.4014 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4014 r_free = 0.4014 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4014 r_free = 0.4014 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6351 moved from start: 0.2929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 4998 Z= 0.130 Angle : 0.774 11.410 6815 Z= 0.385 Chirality : 0.048 0.232 763 Planarity : 0.005 0.049 867 Dihedral : 6.384 59.661 777 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 12.69 Ramachandran Plot: Outliers : 0.16 % Allowed : 14.29 % Favored : 85.55 % Rotamer: Outliers : 2.06 % Allowed : 22.06 % Favored : 75.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.06 (0.30), residues: 616 helix: -3.54 (0.65), residues: 27 sheet: -2.35 (0.39), residues: 167 loop : -2.98 (0.27), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 38 TYR 0.017 0.001 TYR H 96 PHE 0.034 0.002 PHE H 27 TRP 0.017 0.001 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00300 ( 4984) covalent geometry : angle 0.75294 ( 6782) SS BOND : bond 0.00460 ( 9) SS BOND : angle 1.21709 ( 18) hydrogen bonds : bond 0.03288 ( 68) hydrogen bonds : angle 6.71336 ( 171) link_ALPHA1-3 : bond 0.01137 ( 1) link_ALPHA1-3 : angle 1.65530 ( 3) link_ALPHA1-6 : bond 0.00762 ( 1) link_ALPHA1-6 : angle 2.17274 ( 3) link_BETA1-4 : bond 0.00811 ( 2) link_BETA1-4 : angle 1.34303 ( 6) link_NAG-ASN : bond 0.00503 ( 1) link_NAG-ASN : angle 7.74366 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1232 Ramachandran restraints generated. 616 Oldfield, 0 Emsley, 616 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 75 time to evaluate : 0.177 Fit side-chains REVERT: A 402 ILE cc_start: 0.8873 (mp) cc_final: 0.8652 (mm) REVERT: H 72 ASP cc_start: 0.8067 (t0) cc_final: 0.7760 (t0) REVERT: H 100 PHE cc_start: 0.7201 (OUTLIER) cc_final: 0.6948 (t80) REVERT: H 144 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.7471 (m-30) REVERT: L 117 ILE cc_start: 0.7165 (tt) cc_final: 0.6687 (tp) REVERT: L 175 LEU cc_start: 0.7716 (OUTLIER) cc_final: 0.7470 (mt) outliers start: 11 outliers final: 7 residues processed: 82 average time/residue: 0.0859 time to fit residues: 8.8129 Evaluate side-chains 81 residues out of total 536 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 71 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 449 TYR Chi-restraints excluded: chain A residue 470 THR Chi-restraints excluded: chain H residue 100 PHE Chi-restraints excluded: chain H residue 144 ASP Chi-restraints excluded: chain H residue 169 VAL Chi-restraints excluded: chain L residue 175 LEU Chi-restraints excluded: chain L residue 180 THR Chi-restraints excluded: chain L residue 181 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 0.7980 chunk 5 optimal weight: 0.9980 chunk 55 optimal weight: 0.5980 chunk 34 optimal weight: 2.9990 chunk 51 optimal weight: 0.7980 chunk 57 optimal weight: 4.9990 chunk 8 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.2980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4069 r_free = 0.4069 target = 0.093863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3901 r_free = 0.3901 target = 0.085465 restraints weight = 23181.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3938 r_free = 0.3938 target = 0.087257 restraints weight = 14404.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3963 r_free = 0.3963 target = 0.088498 restraints weight = 9915.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 45)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.089346 restraints weight = 7281.734| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3991 r_free = 0.3991 target = 0.089963 restraints weight = 5664.431| |-----------------------------------------------------------------------------| r_work (final): 0.3992 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3992 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3992 r_free = 0.3992 target_work(ls_wunit_k1) = 0.090 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3992 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6389 moved from start: 0.2967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 4998 Z= 0.150 Angle : 0.801 11.421 6815 Z= 0.400 Chirality : 0.048 0.213 763 Planarity : 0.005 0.048 867 Dihedral : 6.337 58.051 777 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 13.21 Ramachandran Plot: Outliers : 0.16 % Allowed : 16.40 % Favored : 83.44 % Rotamer: Outliers : 2.06 % Allowed : 23.55 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -4.13 (0.31), residues: 616 helix: -3.41 (0.68), residues: 27 sheet: -2.37 (0.39), residues: 171 loop : -3.05 (0.27), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 71 TYR 0.013 0.001 TYR L 140 PHE 0.034 0.002 PHE H 27 TRP 0.037 0.002 TRP H 47 HIS 0.003 0.001 HIS L 198 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 4984) covalent geometry : angle 0.77243 ( 6782) SS BOND : bond 0.00496 ( 9) SS BOND : angle 2.47369 ( 18) hydrogen bonds : bond 0.03435 ( 68) hydrogen bonds : angle 6.73167 ( 171) link_ALPHA1-3 : bond 0.01122 ( 1) link_ALPHA1-3 : angle 1.85496 ( 3) link_ALPHA1-6 : bond 0.00886 ( 1) link_ALPHA1-6 : angle 2.11493 ( 3) link_BETA1-4 : bond 0.00773 ( 2) link_BETA1-4 : angle 1.38898 ( 6) link_NAG-ASN : bond 0.00591 ( 1) link_NAG-ASN : angle 7.69171 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1286.57 seconds wall clock time: 22 minutes 52.62 seconds (1372.62 seconds total)