Starting phenix.real_space_refine on Wed Jul 1 21:08:35 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8ea0_27970/07_2026/8ea0_27970.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ea0_27970/07_2026/8ea0_27970.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.56 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/8ea0_27970/07_2026/8ea0_27970.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8ea0_27970/07_2026/8ea0_27970.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ea0_27970/07_2026/8ea0_27970.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ea0_27970/07_2026/8ea0_27970.map" model { file = "/net/cci-nas-00/data/ceres_data/8ea0_27970/07_2026/8ea0_27970.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ea0_27970/07_2026/8ea0_27970.cif" } resolution = 2.56 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= -0.000 sd= 0.015 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 17 5.16 5 C 1531 2.51 5 N 355 2.21 5 O 383 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2286 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2237 Number of conformers: 1 Conformer: "" Number of residues, atoms: 285, 2237 Classifications: {'peptide': 285} Incomplete info: {'truncation_to_alanine': 13} Link IDs: {'PTRANS': 9, 'TRANS': 275} Chain breaks: 1 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 53 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'HIS:plan': 1, 'TRP:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 21 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 49 Unusual residues: {'IXO': 1, 'Y01': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 0.69, per 1000 atoms: 0.30 Number of scatterers: 2286 At special positions: 0 Unit cell: (64.24, 74.8, 68.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 17 16.00 O 383 8.00 N 355 7.00 C 1531 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 141 " - pdb=" SG CYS A 221 " distance=2.03 Simple disulfide: pdb=" SG CYS A 517 " - pdb=" SG CYS A 520 " 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 Time building additional restraints: 0.19 Conformation dependent library (CDL) restraints added in 55.3 milliseconds 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 546 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 0 sheets defined 85.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'A' and resid 64 through 96 removed outlier: 3.604A pdb=" N VAL A 68 " --> pdb=" O THR A 64 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N VAL A 69 " --> pdb=" O VAL A 65 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N PHE A 70 " --> pdb=" O TRP A 66 " (cutoff:3.500A) removed outlier: 5.125A pdb=" N ILE A 71 " --> pdb=" O GLN A 67 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA A 72 " --> pdb=" O VAL A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 101 through 103 No H-bonds generated for 'chain 'A' and resid 101 through 103' Processing helix chain 'A' and resid 104 through 120 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.864A pdb=" N THR A 126 " --> pdb=" O MET A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 172 removed outlier: 3.560A pdb=" N CYS A 141 " --> pdb=" O GLY A 137 " (cutoff:3.500A) removed outlier: 3.731A pdb=" N ASP A 142 " --> pdb=" O ASN A 138 " (cutoff:3.500A) removed outlier: 5.778A pdb=" N LEU A 143 " --> pdb=" O LEU A 139 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N TRP A 144 " --> pdb=" O ALA A 140 " (cutoff:3.500A) Processing helix chain 'A' and resid 175 through 180 removed outlier: 3.824A pdb=" N LYS A 179 " --> pdb=" O THR A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 181 through 211 removed outlier: 4.034A pdb=" N VAL A 187 " --> pdb=" O LYS A 183 " (cutoff:3.500A) removed outlier: 3.516A pdb=" N MET A 188 " --> pdb=" O ARG A 184 " (cutoff:3.500A) removed outlier: 4.328A pdb=" N TRP A 200 " --> pdb=" O SER A 196 " (cutoff:3.500A) Proline residue: A 202 - end of helix removed outlier: 5.186A pdb=" N GLN A 208 " --> pdb=" O ILE A 204 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N TYR A 209 " --> pdb=" O LEU A 205 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 240 Processing helix chain 'A' and resid 240 through 265 removed outlier: 3.511A pdb=" N GLU A 257 " --> pdb=" O ARG A 253 " (cutoff:3.500A) Processing helix chain 'A' and resid 488 through 503 Processing helix chain 'A' and resid 504 through 517 removed outlier: 4.035A pdb=" N LEU A 512 " --> pdb=" O ASN A 508 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N THR A 515 " --> pdb=" O VAL A 511 " (cutoff:3.500A) removed outlier: 3.667A pdb=" N PHE A 516 " --> pdb=" O LEU A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 522 through 534 removed outlier: 3.541A pdb=" N CYS A 533 " --> pdb=" O GLY A 529 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N TYR A 534 " --> pdb=" O TYR A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 545 removed outlier: 3.570A pdb=" N THR A 538 " --> pdb=" O TYR A 534 " (cutoff:3.500A) Proline residue: A 541 - end of helix Processing helix chain 'A' and resid 548 through 561 160 hydrogen bonds defined for protein. 480 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: 0.24 Time building geometry restraints manager: 0.22 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 330 1.31 - 1.43: 665 1.43 - 1.56: 1328 1.56 - 1.68: 0 1.68 - 1.81: 24 Bond restraints: 2347 Sorted by residual: bond pdb=" CAY Y01 A 802 " pdb=" OAW Y01 A 802 " ideal model delta sigma weight residual 1.332 1.376 -0.044 2.00e-02 2.50e+03 4.91e+00 bond pdb=" N11 IXO A 801 " pdb=" O12 IXO A 801 " ideal model delta sigma weight residual 1.385 1.425 -0.040 2.00e-02 2.50e+03 3.91e+00 bond pdb=" C10 IXO A 801 " pdb=" N11 IXO A 801 " ideal model delta sigma weight residual 1.270 1.307 -0.037 2.00e-02 2.50e+03 3.35e+00 bond pdb=" CBC Y01 A 802 " pdb=" OAW Y01 A 802 " ideal model delta sigma weight residual 1.437 1.417 0.020 2.00e-02 2.50e+03 9.92e-01 bond pdb=" CAX Y01 A 802 " pdb=" OAF Y01 A 802 " ideal model delta sigma weight residual 1.247 1.266 -0.019 2.00e-02 2.50e+03 8.76e-01 ... (remaining 2342 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.40: 3130 1.40 - 2.81: 57 2.81 - 4.21: 16 4.21 - 5.61: 8 5.61 - 7.02: 3 Bond angle restraints: 3214 Sorted by residual: angle pdb=" CBB Y01 A 802 " pdb=" CBE Y01 A 802 " pdb=" CBI Y01 A 802 " ideal model delta sigma weight residual 119.27 112.25 7.02 3.00e+00 1.11e-01 5.47e+00 angle pdb=" CAJ Y01 A 802 " pdb=" CAO Y01 A 802 " pdb=" CBB Y01 A 802 " ideal model delta sigma weight residual 115.08 108.22 6.86 3.00e+00 1.11e-01 5.23e+00 angle pdb=" C PHE A 197 " pdb=" N VAL A 198 " pdb=" CA VAL A 198 " ideal model delta sigma weight residual 121.97 118.19 3.78 1.80e+00 3.09e-01 4.41e+00 angle pdb=" N LEU A 199 " pdb=" CA LEU A 199 " pdb=" C LEU A 199 " ideal model delta sigma weight residual 114.62 112.39 2.23 1.14e+00 7.69e-01 3.83e+00 angle pdb=" CAL Y01 A 802 " pdb=" CAM Y01 A 802 " pdb=" CAY Y01 A 802 " ideal model delta sigma weight residual 113.76 108.11 5.65 3.00e+00 1.11e-01 3.55e+00 ... (remaining 3209 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.23: 1229 17.23 - 34.46: 99 34.46 - 51.70: 17 51.70 - 68.93: 2 68.93 - 86.16: 1 Dihedral angle restraints: 1348 sinusoidal: 506 harmonic: 842 Sorted by residual: dihedral pdb=" CB CYS A 517 " pdb=" SG CYS A 517 " pdb=" SG CYS A 520 " pdb=" CB CYS A 520 " ideal model delta sinusoidal sigma weight residual 93.00 179.16 -86.16 1 1.00e+01 1.00e-02 8.96e+01 dihedral pdb=" CA VAL A 198 " pdb=" C VAL A 198 " pdb=" N LEU A 199 " pdb=" CA LEU A 199 " ideal model delta harmonic sigma weight residual 180.00 157.94 22.06 0 5.00e+00 4.00e-02 1.95e+01 dihedral pdb=" CA ARG A 261 " pdb=" CB ARG A 261 " pdb=" CG ARG A 261 " pdb=" CD ARG A 261 " ideal model delta sinusoidal sigma weight residual -60.00 -112.14 52.14 3 1.50e+01 4.44e-03 9.09e+00 ... (remaining 1345 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 363 0.067 - 0.134: 24 0.134 - 0.202: 0 0.202 - 0.269: 1 0.269 - 0.336: 2 Chirality restraints: 390 Sorted by residual: chirality pdb=" CBG Y01 A 802 " pdb=" CAQ Y01 A 802 " pdb=" CBD Y01 A 802 " pdb=" CBI Y01 A 802 " both_signs ideal model delta sigma weight residual False -2.33 -2.67 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CBF Y01 A 802 " pdb=" CAS Y01 A 802 " pdb=" CBD Y01 A 802 " pdb=" CBH Y01 A 802 " both_signs ideal model delta sigma weight residual False -2.45 -2.73 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" CBE Y01 A 802 " pdb=" CAP Y01 A 802 " pdb=" CBB Y01 A 802 " pdb=" CBI Y01 A 802 " both_signs ideal model delta sigma weight residual False 2.57 2.79 -0.23 2.00e-01 2.50e+01 1.27e+00 ... (remaining 387 not shown) Planarity restraints: 375 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 225 " 0.011 2.00e-02 2.50e+03 9.62e-03 1.62e+00 pdb=" CG PHE A 225 " -0.022 2.00e-02 2.50e+03 pdb=" CD1 PHE A 225 " 0.004 2.00e-02 2.50e+03 pdb=" CD2 PHE A 225 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 PHE A 225 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 225 " 0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 225 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 242 " -0.017 5.00e-02 4.00e+02 2.56e-02 1.05e+00 pdb=" N PRO A 243 " 0.044 5.00e-02 4.00e+02 pdb=" CA PRO A 243 " -0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 243 " -0.014 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 133 " 0.083 9.50e-02 1.11e+02 3.71e-02 8.49e-01 pdb=" NE ARG A 133 " -0.005 2.00e-02 2.50e+03 pdb=" CZ ARG A 133 " 0.000 2.00e-02 2.50e+03 pdb=" NH1 ARG A 133 " -0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG A 133 " 0.003 2.00e-02 2.50e+03 ... (remaining 372 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 444 2.77 - 3.30: 2235 3.30 - 3.83: 3720 3.83 - 4.37: 4384 4.37 - 4.90: 7587 Nonbonded interactions: 18370 Sorted by model distance: nonbonded pdb=" OG1 THR A 82 " pdb=" OG1 THR A 538 " model vdw 2.237 3.040 nonbonded pdb=" O ILE A 501 " pdb=" OG1 THR A 505 " model vdw 2.282 3.040 nonbonded pdb=" O ILE A 246 " pdb=" CD1 LEU A 250 " model vdw 2.286 3.460 nonbonded pdb=" O VAL A 119 " pdb=" ND2 ASN A 123 " model vdw 2.341 3.120 nonbonded pdb=" OE1 GLN A 208 " pdb=" NE ARG A 214 " model vdw 2.346 3.120 ... (remaining 18365 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: 1.800 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.440 Find NCS groups from input model: 0.020 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:9.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 2349 Z= 0.135 Angle : 0.555 7.018 3218 Z= 0.253 Chirality : 0.045 0.336 390 Planarity : 0.004 0.037 375 Dihedral : 12.240 58.490 796 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.00 % Allowed : 0.42 % Favored : 99.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -0.24 (0.51), residues: 281 helix: 0.28 (0.35), residues: 218 sheet: None (None), residues: 0 loop : -1.38 (0.87), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 180 TYR 0.006 0.001 TYR A 241 PHE 0.022 0.001 PHE A 225 TRP 0.005 0.001 TRP A 531 Details of bonding type rmsd/Z covalent geometry : bond 0.00283 / 0.14 ( 2347) covalent geometry : angle 0.55466 / 0.25 ( 3214) SS BOND : bond 0.00384 / 0.26 ( 2) SS BOND : angle 0.48657 / 0.36 ( 4) hydrogen bonds : bond 0.26243 / 17.38 ( 160) hydrogen bonds : angle 8.44156 / 6.33 ( 480) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.106 Fit side-chains REVERT: A 525 PHE cc_start: 0.7945 (m-80) cc_final: 0.7540 (m-80) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.3184 time to fit residues: 16.0936 Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 27 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.4980 chunk 13 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 16 optimal weight: 0.0050 chunk 15 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 0.8980 chunk 9 optimal weight: 0.2980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 132 ASN A 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3834 r_free = 0.3834 target = 0.134238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3648 r_free = 0.3648 target = 0.119940 restraints weight = 2985.347| |-----------------------------------------------------------------------------| r_work (start): 0.3644 rms_B_bonded: 1.51 r_work: 0.3546 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3411 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 moved from start: 0.1879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2349 Z= 0.187 Angle : 0.594 5.604 3218 Z= 0.313 Chirality : 0.043 0.137 390 Planarity : 0.005 0.032 375 Dihedral : 7.025 55.238 325 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.94 % Allowed : 8.40 % Favored : 88.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 0.87 (0.53), residues: 281 helix: 1.17 (0.35), residues: 220 sheet: None (None), residues: 0 loop : -1.51 (0.92), residues: 61 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 253 TYR 0.011 0.002 TYR A 530 PHE 0.032 0.002 PHE A 225 TRP 0.009 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.19 ( 2347) covalent geometry : angle 0.59388 / 0.31 ( 3214) SS BOND : bond 0.00767 / 0.51 ( 2) SS BOND : angle 0.80100 / 0.55 ( 4) hydrogen bonds : bond 0.05995 / 3.97 ( 160) hydrogen bonds : angle 4.98112 / 3.80 ( 480) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 39 time to evaluate : 0.052 Fit side-chains REVERT: A 180 ARG cc_start: 0.8217 (OUTLIER) cc_final: 0.8016 (ttp-110) REVERT: A 525 PHE cc_start: 0.8254 (m-80) cc_final: 0.7765 (m-80) outliers start: 7 outliers final: 2 residues processed: 42 average time/residue: 0.3939 time to fit residues: 16.9816 Evaluate side-chains 39 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 36 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 131 MET Chi-restraints excluded: chain A residue 180 ARG Chi-restraints excluded: chain A residue 524 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 7 optimal weight: 0.0570 chunk 26 optimal weight: 0.2980 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 18 optimal weight: 0.2980 chunk 24 optimal weight: 0.1980 chunk 2 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 6 optimal weight: 0.3980 chunk 23 optimal weight: 0.0980 chunk 10 optimal weight: 0.2980 overall best weight: 0.1898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3855 r_free = 0.3855 target = 0.136064 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.122000 restraints weight = 3003.252| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 1.49 r_work: 0.3583 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2206 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.019 2349 Z= 0.124 Angle : 0.516 5.489 3218 Z= 0.274 Chirality : 0.039 0.129 390 Planarity : 0.004 0.027 375 Dihedral : 6.975 58.158 325 Min Nonbonded Distance : 2.637 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.98 % Favored : 95.02 % Rotamer: Outliers : 2.94 % Allowed : 10.50 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 1.20 (0.53), residues: 281 helix: 1.62 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.81 (0.80), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 133 TYR 0.010 0.001 TYR A 544 PHE 0.026 0.001 PHE A 225 TRP 0.007 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00256 / 0.12 ( 2347) covalent geometry : angle 0.51562 / 0.27 ( 3214) SS BOND : bond 0.00518 / 0.35 ( 2) SS BOND : angle 0.56993 / 0.39 ( 4) hydrogen bonds : bond 0.04731 / 3.19 ( 160) hydrogen bonds : angle 4.63033 / 3.57 ( 480) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.084 Fit side-chains REVERT: A 488 LYS cc_start: 0.7867 (OUTLIER) cc_final: 0.7384 (mtmm) REVERT: A 525 PHE cc_start: 0.8263 (m-80) cc_final: 0.7830 (m-80) outliers start: 7 outliers final: 1 residues processed: 45 average time/residue: 0.3323 time to fit residues: 15.4262 Evaluate side-chains 41 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 39 time to evaluate : 0.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 232 THR Chi-restraints excluded: chain A residue 488 LYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 24 optimal weight: 0.0870 chunk 6 optimal weight: 0.5980 chunk 8 optimal weight: 0.0770 chunk 2 optimal weight: 0.0970 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 14 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 11 optimal weight: 0.4980 chunk 9 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 overall best weight: 0.2114 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3843 r_free = 0.3843 target = 0.135502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121397 restraints weight = 3056.737| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.48 r_work: 0.3575 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3444 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3444 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8035 moved from start: 0.2305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2349 Z= 0.131 Angle : 0.520 5.303 3218 Z= 0.276 Chirality : 0.039 0.129 390 Planarity : 0.004 0.029 375 Dihedral : 6.978 58.919 325 Min Nonbonded Distance : 2.621 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.52 % Allowed : 12.61 % Favored : 84.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 1.29 (0.54), residues: 281 helix: 1.72 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.91 (0.79), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.010 0.001 TYR A 544 PHE 0.023 0.001 PHE A 225 TRP 0.006 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 2347) covalent geometry : angle 0.51971 / 0.28 ( 3214) SS BOND : bond 0.00508 / 0.34 ( 2) SS BOND : angle 0.50584 / 0.35 ( 4) hydrogen bonds : bond 0.04571 / 3.08 ( 160) hydrogen bonds : angle 4.50498 / 3.46 ( 480) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.049 Fit side-chains REVERT: A 488 LYS cc_start: 0.7914 (OUTLIER) cc_final: 0.7456 (mtmm) REVERT: A 525 PHE cc_start: 0.8271 (m-80) cc_final: 0.7847 (m-80) outliers start: 6 outliers final: 1 residues processed: 44 average time/residue: 0.3522 time to fit residues: 15.9155 Evaluate side-chains 42 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 488 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.2980 chunk 4 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 24 optimal weight: 0.2980 chunk 5 optimal weight: 0.3980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.4580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.135565 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.121463 restraints weight = 2962.866| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 1.48 r_work: 0.3576 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3446 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3446 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.2357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2349 Z= 0.131 Angle : 0.520 5.303 3218 Z= 0.276 Chirality : 0.039 0.129 390 Planarity : 0.004 0.029 375 Dihedral : 6.978 58.919 325 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 0.84 % Allowed : 15.97 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 1.29 (0.54), residues: 281 helix: 1.72 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.91 (0.79), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.010 0.001 TYR A 544 PHE 0.023 0.001 PHE A 225 TRP 0.006 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00284 / 0.13 ( 2347) covalent geometry : angle 0.51971 / 0.28 ( 3214) SS BOND : bond 0.00508 / 0.34 ( 2) SS BOND : angle 0.50584 / 0.35 ( 4) hydrogen bonds : bond 0.04571 / 3.08 ( 160) hydrogen bonds : angle 4.50498 / 3.46 ( 480) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.084 Fit side-chains REVERT: A 488 LYS cc_start: 0.7908 (OUTLIER) cc_final: 0.7447 (mtmm) REVERT: A 525 PHE cc_start: 0.8272 (m-80) cc_final: 0.7847 (m-80) outliers start: 2 outliers final: 1 residues processed: 42 average time/residue: 0.3985 time to fit residues: 17.2326 Evaluate side-chains 42 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 488 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.3980 chunk 16 optimal weight: 0.0070 chunk 11 optimal weight: 0.8980 chunk 22 optimal weight: 0.3980 chunk 20 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 7 optimal weight: 0.2980 overall best weight: 0.3398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 132 ASN A 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3832 r_free = 0.3832 target = 0.134800 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.120728 restraints weight = 2978.172| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.48 r_work: 0.3570 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3438 rms_B_bonded: 3.82 restraints_weight: 0.2500 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2349 Z= 0.158 Angle : 0.539 5.437 3218 Z= 0.286 Chirality : 0.040 0.132 390 Planarity : 0.004 0.032 375 Dihedral : 7.027 58.627 325 Min Nonbonded Distance : 2.583 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.52 % Allowed : 13.45 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 1.25 (0.54), residues: 281 helix: 1.70 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.94 (0.79), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.010 0.001 TYR A 530 PHE 0.022 0.001 PHE A 225 TRP 0.006 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00361 / 0.16 ( 2347) covalent geometry : angle 0.53894 / 0.29 ( 3214) SS BOND : bond 0.00687 / 0.46 ( 2) SS BOND : angle 0.62001 / 0.43 ( 4) hydrogen bonds : bond 0.04745 / 3.17 ( 160) hydrogen bonds : angle 4.46676 / 3.43 ( 480) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.084 Fit side-chains REVERT: A 488 LYS cc_start: 0.7937 (OUTLIER) cc_final: 0.7478 (mtmm) REVERT: A 525 PHE cc_start: 0.8279 (m-80) cc_final: 0.7874 (m-80) REVERT: A 528 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8426 (tt) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.3031 time to fit residues: 13.1069 Evaluate side-chains 44 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 14 optimal weight: 0.0980 chunk 2 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 11 optimal weight: 0.1980 chunk 15 optimal weight: 0.6980 chunk 7 optimal weight: 0.6980 chunk 6 optimal weight: 0.1980 chunk 9 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 132 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3833 r_free = 0.3833 target = 0.134994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3657 r_free = 0.3657 target = 0.120894 restraints weight = 3002.870| |-----------------------------------------------------------------------------| r_work (start): 0.3662 rms_B_bonded: 1.49 r_work: 0.3569 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3436 rms_B_bonded: 3.85 restraints_weight: 0.2500 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8047 moved from start: 0.2441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 2349 Z= 0.158 Angle : 0.539 5.435 3218 Z= 0.286 Chirality : 0.040 0.129 390 Planarity : 0.004 0.032 375 Dihedral : 7.099 58.627 325 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.10 % Allowed : 15.13 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 1.25 (0.54), residues: 281 helix: 1.70 (0.37), residues: 211 sheet: None (None), residues: 0 loop : -1.94 (0.79), residues: 70 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 180 TYR 0.010 0.001 TYR A 530 PHE 0.022 0.001 PHE A 225 TRP 0.006 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00362 / 0.16 ( 2347) covalent geometry : angle 0.53852 / 0.29 ( 3214) SS BOND : bond 0.00684 / 0.46 ( 2) SS BOND : angle 0.62040 / 0.43 ( 4) hydrogen bonds : bond 0.04746 / 3.17 ( 160) hydrogen bonds : angle 4.46727 / 3.43 ( 480) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 38 time to evaluate : 0.050 Fit side-chains REVERT: A 488 LYS cc_start: 0.7946 (OUTLIER) cc_final: 0.7492 (mtmm) REVERT: A 525 PHE cc_start: 0.8281 (m-80) cc_final: 0.7877 (m-80) REVERT: A 528 LEU cc_start: 0.8650 (OUTLIER) cc_final: 0.8427 (tt) outliers start: 5 outliers final: 4 residues processed: 41 average time/residue: 0.3050 time to fit residues: 12.8357 Evaluate side-chains 44 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 38 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 132 ASN Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 10 optimal weight: 0.3980 chunk 23 optimal weight: 0.7980 chunk 19 optimal weight: 0.2980 chunk 15 optimal weight: 0.3980 chunk 5 optimal weight: 0.9990 chunk 7 optimal weight: 0.4980 chunk 16 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.134275 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.120300 restraints weight = 2966.340| |-----------------------------------------------------------------------------| r_work (start): 0.3654 rms_B_bonded: 1.47 r_work: 0.3562 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 3.78 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.2459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 2349 Z= 0.178 Angle : 0.553 5.491 3218 Z= 0.292 Chirality : 0.042 0.138 390 Planarity : 0.004 0.033 375 Dihedral : 7.058 58.562 325 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 2.52 % Allowed : 14.71 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 1.27 (0.54), residues: 281 helix: 1.59 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -1.72 (0.86), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 180 TYR 0.011 0.002 TYR A 530 PHE 0.021 0.001 PHE A 225 TRP 0.006 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00417 / 0.18 ( 2347) covalent geometry : angle 0.55309 / 0.29 ( 3214) SS BOND : bond 0.00769 / 0.51 ( 2) SS BOND : angle 0.66703 / 0.48 ( 4) hydrogen bonds : bond 0.04916 / 3.26 ( 160) hydrogen bonds : angle 4.46246 / 3.43 ( 480) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.062 Fit side-chains REVERT: A 488 LYS cc_start: 0.7967 (OUTLIER) cc_final: 0.7502 (mtmm) REVERT: A 525 PHE cc_start: 0.8273 (m-80) cc_final: 0.7884 (m-80) REVERT: A 528 LEU cc_start: 0.8669 (OUTLIER) cc_final: 0.8440 (tt) outliers start: 6 outliers final: 3 residues processed: 43 average time/residue: 0.2951 time to fit residues: 13.0515 Evaluate side-chains 44 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 39 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 23 optimal weight: 0.0770 chunk 20 optimal weight: 0.8980 chunk 4 optimal weight: 0.6980 chunk 27 optimal weight: 0.8980 chunk 6 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 16 optimal weight: 0.4980 chunk 9 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 26 optimal weight: 0.6980 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 132 ASN A 536 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.132807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3631 r_free = 0.3631 target = 0.118987 restraints weight = 3051.074| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.48 r_work: 0.3541 rms_B_bonded: 2.13 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 3.77 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8082 moved from start: 0.2636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.060 2349 Z= 0.206 Angle : 0.600 5.649 3218 Z= 0.319 Chirality : 0.043 0.130 390 Planarity : 0.005 0.040 375 Dihedral : 7.341 59.211 325 Min Nonbonded Distance : 2.615 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 2.52 % Allowed : 16.39 % Favored : 81.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 1.15 (0.54), residues: 281 helix: 1.46 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -1.63 (0.86), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG A 180 TYR 0.012 0.002 TYR A 530 PHE 0.022 0.002 PHE A 225 TRP 0.007 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00493 / 0.21 ( 2347) covalent geometry : angle 0.59950 / 0.32 ( 3214) SS BOND : bond 0.00950 / 0.63 ( 2) SS BOND : angle 0.85869 / 0.60 ( 4) hydrogen bonds : bond 0.05221 / 3.45 ( 160) hydrogen bonds : angle 4.52835 / 3.46 ( 480) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.050 Fit side-chains REVERT: A 488 LYS cc_start: 0.8038 (OUTLIER) cc_final: 0.7463 (mtmm) REVERT: A 525 PHE cc_start: 0.8294 (m-80) cc_final: 0.7982 (m-80) REVERT: A 528 LEU cc_start: 0.8683 (OUTLIER) cc_final: 0.8449 (tt) outliers start: 6 outliers final: 4 residues processed: 42 average time/residue: 0.2809 time to fit residues: 12.1453 Evaluate side-chains 45 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 242 MET Chi-restraints excluded: chain A residue 488 LYS Chi-restraints excluded: chain A residue 503 THR Chi-restraints excluded: chain A residue 528 LEU Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 15 optimal weight: 0.3980 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.1980 chunk 3 optimal weight: 0.3980 chunk 22 optimal weight: 0.1980 chunk 25 optimal weight: 0.2980 chunk 23 optimal weight: 0.0970 chunk 7 optimal weight: 0.0980 chunk 13 optimal weight: 0.4980 chunk 26 optimal weight: 0.9980 chunk 6 optimal weight: 0.4980 overall best weight: 0.1778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3847 r_free = 0.3847 target = 0.135865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.122317 restraints weight = 3011.748| |-----------------------------------------------------------------------------| r_work (start): 0.3681 rms_B_bonded: 1.45 r_work: 0.3592 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3463 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3463 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.2781 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 2349 Z= 0.132 Angle : 0.526 5.367 3218 Z= 0.282 Chirality : 0.039 0.144 390 Planarity : 0.004 0.031 375 Dihedral : 7.096 58.942 325 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 1.68 % Allowed : 15.55 % Favored : 82.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 1.44 (0.54), residues: 281 helix: 1.70 (0.37), residues: 217 sheet: None (None), residues: 0 loop : -1.65 (0.86), residues: 64 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 180 TYR 0.009 0.001 TYR A 530 PHE 0.023 0.001 PHE A 225 TRP 0.007 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.13 ( 2347) covalent geometry : angle 0.52555 / 0.28 ( 3214) SS BOND : bond 0.00596 / 0.40 ( 2) SS BOND : angle 0.60062 / 0.43 ( 4) hydrogen bonds : bond 0.04347 / 2.88 ( 160) hydrogen bonds : angle 4.39286 / 3.38 ( 480) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 562 Ramachandran restraints generated. 281 Oldfield, 0 Emsley, 281 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 40 time to evaluate : 0.056 Fit side-chains REVERT: A 525 PHE cc_start: 0.8281 (m-80) cc_final: 0.8001 (m-80) outliers start: 4 outliers final: 2 residues processed: 42 average time/residue: 0.2691 time to fit residues: 11.6428 Evaluate side-chains 42 residues out of total 251 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.054 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 184 ARG Chi-restraints excluded: chain A residue 550 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 28 random chunks: chunk 25 optimal weight: 0.5980 chunk 17 optimal weight: 0.3980 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 0.6980 chunk 26 optimal weight: 0.0270 chunk 21 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 7 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 overall best weight: 0.3438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 103 ASN A 132 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3835 r_free = 0.3835 target = 0.134966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.121374 restraints weight = 3031.025| |-----------------------------------------------------------------------------| r_work (start): 0.3651 rms_B_bonded: 1.44 r_work: 0.3567 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3441 rms_B_bonded: 3.65 restraints_weight: 0.2500 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.2798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 2349 Z= 0.163 Angle : 0.548 5.468 3218 Z= 0.292 Chirality : 0.042 0.143 390 Planarity : 0.004 0.034 375 Dihedral : 7.133 59.841 325 Min Nonbonded Distance : 2.359 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.63 % Favored : 95.37 % Rotamer: Outliers : 1.68 % Allowed : 18.07 % Favored : 80.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.36 % 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: 1.41 (0.54), residues: 281 helix: 1.72 (0.37), residues: 216 sheet: None (None), residues: 0 loop : -1.78 (0.86), residues: 65 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 133 TYR 0.010 0.002 TYR A 530 PHE 0.046 0.002 PHE A 225 TRP 0.007 0.001 TRP A 252 Details of bonding type rmsd/Z covalent geometry : bond 0.00383 / 0.16 ( 2347) covalent geometry : angle 0.54794 / 0.29 ( 3214) SS BOND : bond 0.00799 / 0.53 ( 2) SS BOND : angle 0.75510 / 0.52 ( 4) hydrogen bonds : bond 0.04589 / 3.03 ( 160) hydrogen bonds : angle 4.41101 / 3.39 ( 480) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 929.76 seconds wall clock time: 16 minutes 31.41 seconds (991.41 seconds total)