Starting phenix.real_space_refine on Wed Sep 17 03:22:46 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9bee_44477/09_2025/9bee_44477_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/9bee_44477/09_2025/9bee_44477.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9bee_44477/09_2025/9bee_44477.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9bee_44477/09_2025/9bee_44477.map" model { file = "/net/cci-nas-00/data/ceres_data/9bee_44477/09_2025/9bee_44477_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9bee_44477/09_2025/9bee_44477_trim.cif" } resolution = 3.4 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= 0.010 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: 5 Type Number sf(0) Gaussians S 1 5.16 5 C 962 2.51 5 N 285 2.21 5 O 297 1.98 5 H 1501 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3046 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 88, 1408 Classifications: {'peptide': 88} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 6, 'TRANS': 81} Chain: "A" Number of atoms: 1638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1638 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 6, 'TRANS': 101} Chain breaks: 1 Unresolved non-hydrogen bonds: 14 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 7 Planarities with less than four sites: {'UNK:plan-1': 7} Unresolved non-hydrogen planarities: 7 Time building chain proxies: 0.88, per 1000 atoms: 0.29 Number of scatterers: 3046 At special positions: 0 Unit cell: (78.012, 43.34, 107.956, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 1 16.00 O 297 8.00 N 285 7.00 C 962 6.00 H 1501 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.24 Conformation dependent library (CDL) restraints added in 66.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 366 Finding SS restraints... Secondary structure from input PDB file: 1 helices and 4 sheets defined 1.6% alpha, 49.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 85 through 87 No H-bonds generated for 'chain 'A' and resid 85 through 87' Processing sheet with id=AA1, first strand: chain 'B' and resid 77 through 80 Processing sheet with id=AA2, first strand: chain 'B' and resid 90 through 94 Processing sheet with id=AA3, first strand: chain 'B' and resid 90 through 94 removed outlier: 3.869A pdb=" N PHE B 113 " --> pdb=" O LYS A 121 " (cutoff:3.500A) removed outlier: 4.339A pdb=" N PHE A 113 " --> pdb=" O LYS B 121 " (cutoff:3.500A) removed outlier: 4.777A pdb=" N ARG A 116 " --> pdb=" O GLU A 105 " (cutoff:3.500A) removed outlier: 4.881A pdb=" N GLU A 105 " --> pdb=" O ARG A 116 " (cutoff:3.500A) removed outlier: 7.521A pdb=" N PHE A 118 " --> pdb=" O LYS A 103 " (cutoff:3.500A) removed outlier: 5.585A pdb=" N LYS A 103 " --> pdb=" O PHE A 118 " (cutoff:3.500A) removed outlier: 7.035A pdb=" N ARG A 120 " --> pdb=" O HIS A 101 " (cutoff:3.500A) removed outlier: 5.187A pdb=" N HIS A 101 " --> pdb=" O ARG A 120 " (cutoff:3.500A) removed outlier: 6.580A pdb=" N TYR A 122 " --> pdb=" O GLU A 99 " (cutoff:3.500A) removed outlier: 4.987A pdb=" N GLU A 99 " --> pdb=" O TYR A 122 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 67 through 70 removed outlier: 3.517A pdb=" N VAL A 142 " --> pdb=" O SER A 138 " (cutoff:3.500A) 63 hydrogen bonds defined for protein. 162 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: 0.54 Time building geometry restraints manager: 0.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.04: 844 1.04 - 1.23: 739 1.23 - 1.42: 562 1.42 - 1.62: 927 1.62 - 1.81: 2 Bond restraints: 3074 Sorted by residual: bond pdb=" N ARG B 116 " pdb=" H ARG B 116 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU B 143 " pdb=" H LEU B 143 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" CD2 TYR B 122 " pdb=" HD2 TYR B 122 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N ILE B 159 " pdb=" H ILE B 159 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.68e+01 bond pdb=" N SER B 135 " pdb=" H SER B 135 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.67e+01 ... (remaining 3069 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 3823 1.60 - 3.20: 1311 3.20 - 4.80: 295 4.80 - 6.41: 91 6.41 - 8.01: 38 Bond angle restraints: 5558 Sorted by residual: angle pdb=" CA ARG A 116 " pdb=" C ARG A 116 " pdb=" O ARG A 116 " ideal model delta sigma weight residual 121.06 115.75 5.31 1.16e+00 7.43e-01 2.09e+01 angle pdb=" CA GLY A 154 " pdb=" C GLY A 154 " pdb=" O GLY A 154 " ideal model delta sigma weight residual 122.46 118.24 4.22 9.70e-01 1.06e+00 1.89e+01 angle pdb=" CA VAL A 97 " pdb=" C VAL A 97 " pdb=" O VAL A 97 " ideal model delta sigma weight residual 121.63 117.64 3.99 9.90e-01 1.02e+00 1.63e+01 angle pdb=" N ARG A 116 " pdb=" CA ARG A 116 " pdb=" CB ARG A 116 " ideal model delta sigma weight residual 111.53 104.26 7.27 1.86e+00 2.89e-01 1.53e+01 angle pdb=" N ASN B 146 " pdb=" CA ASN B 146 " pdb=" CB ASN B 146 " ideal model delta sigma weight residual 111.55 104.91 6.64 1.74e+00 3.30e-01 1.46e+01 ... (remaining 5553 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.55: 1297 15.55 - 31.10: 86 31.10 - 46.65: 25 46.65 - 62.19: 22 62.19 - 77.74: 12 Dihedral angle restraints: 1442 sinusoidal: 803 harmonic: 639 Sorted by residual: dihedral pdb=" C GLU B 156 " pdb=" N GLU B 156 " pdb=" CA GLU B 156 " pdb=" CB GLU B 156 " ideal model delta harmonic sigma weight residual -122.60 -132.55 9.95 0 2.50e+00 1.60e-01 1.58e+01 dihedral pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CA GLU B 156 " pdb=" CB GLU B 156 " ideal model delta harmonic sigma weight residual 122.80 131.93 -9.13 0 2.50e+00 1.60e-01 1.33e+01 dihedral pdb=" C VAL B 142 " pdb=" N VAL B 142 " pdb=" CA VAL B 142 " pdb=" CB VAL B 142 " ideal model delta harmonic sigma weight residual -122.00 -129.65 7.65 0 2.50e+00 1.60e-01 9.36e+00 ... (remaining 1439 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 123 0.067 - 0.135: 72 0.135 - 0.202: 37 0.202 - 0.270: 7 0.270 - 0.337: 1 Chirality restraints: 240 Sorted by residual: chirality pdb=" CA GLU B 156 " pdb=" N GLU B 156 " pdb=" C GLU B 156 " pdb=" CB GLU B 156 " both_signs ideal model delta sigma weight residual False 2.51 2.17 0.34 2.00e-01 2.50e+01 2.84e+00 chirality pdb=" CA PRO A 86 " pdb=" N PRO A 86 " pdb=" C PRO A 86 " pdb=" CB PRO A 86 " both_signs ideal model delta sigma weight residual False 2.72 2.46 0.26 2.00e-01 2.50e+01 1.68e+00 chirality pdb=" CA UNK A 26 " pdb=" N UNK A 26 " pdb=" C UNK A 26 " pdb=" CB UNK A 26 " both_signs ideal model delta sigma weight residual False 2.52 2.27 0.25 2.00e-01 2.50e+01 1.56e+00 ... (remaining 237 not shown) Planarity restraints: 453 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 116 " -0.030 9.50e-02 1.11e+02 6.55e-02 9.43e+01 pdb=" NE ARG B 116 " 0.056 2.00e-02 2.50e+03 pdb=" CZ ARG B 116 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG B 116 " -0.101 2.00e-02 2.50e+03 pdb=" NH2 ARG B 116 " 0.027 2.00e-02 2.50e+03 pdb="HH11 ARG B 116 " -0.042 2.00e-02 2.50e+03 pdb="HH12 ARG B 116 " 0.136 2.00e-02 2.50e+03 pdb="HH21 ARG B 116 " -0.006 2.00e-02 2.50e+03 pdb="HH22 ARG B 116 " -0.058 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 107 " 0.024 9.50e-02 1.11e+02 5.15e-02 5.82e+01 pdb=" NE ARG B 107 " -0.025 2.00e-02 2.50e+03 pdb=" CZ ARG B 107 " -0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 107 " -0.039 2.00e-02 2.50e+03 pdb=" NH2 ARG B 107 " 0.028 2.00e-02 2.50e+03 pdb="HH11 ARG B 107 " 0.006 2.00e-02 2.50e+03 pdb="HH12 ARG B 107 " 0.077 2.00e-02 2.50e+03 pdb="HH21 ARG B 107 " 0.067 2.00e-02 2.50e+03 pdb="HH22 ARG B 107 " -0.098 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 146 " 0.056 2.00e-02 2.50e+03 6.03e-02 5.45e+01 pdb=" CG ASN A 146 " 0.002 2.00e-02 2.50e+03 pdb=" OD1 ASN A 146 " -0.057 2.00e-02 2.50e+03 pdb=" ND2 ASN A 146 " -0.002 2.00e-02 2.50e+03 pdb="HD21 ASN A 146 " 0.089 2.00e-02 2.50e+03 pdb="HD22 ASN A 146 " -0.087 2.00e-02 2.50e+03 ... (remaining 450 not shown) Histogram of nonbonded interaction distances: 1.62 - 2.22: 224 2.22 - 2.81: 5994 2.81 - 3.41: 7524 3.41 - 4.00: 9812 4.00 - 4.60: 14142 Nonbonded interactions: 37696 Sorted by model distance: nonbonded pdb=" HG SER A 85 " pdb=" OE1 GLU A 88 " model vdw 1.620 2.450 nonbonded pdb=" OD1 ASN B 78 " pdb=" HG1 THR B 144 " model vdw 1.691 2.450 nonbonded pdb=" O VAL B 81 " pdb=" H PHE B 84 " model vdw 1.698 2.450 nonbonded pdb=" OE1 GLU B 99 " pdb=" HZ3 LYS B 121 " model vdw 1.763 2.450 nonbonded pdb=" OE1 GLU A 87 " pdb=" H GLU A 87 " model vdw 1.792 2.450 ... (remaining 37691 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 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: 1.620 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.030 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 8.200 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5903 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 : 0.013 0.047 1573 Z= 0.927 Angle : 1.844 7.267 2123 Z= 1.233 Chirality : 0.098 0.337 240 Planarity : 0.016 0.100 280 Dihedral : 11.725 76.567 605 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.89 % Favored : 88.11 % Rotamer: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Cbeta Deviations : 0.55 % 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 aren not related in a simple way. whole: -2.32 (0.60), residues: 185 helix: None (None), residues: 0 sheet: -1.28 (0.58), residues: 77 loop : -1.75 (0.59), residues: 108 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.002 ARG B 163 TYR 0.081 0.020 TYR B 122 PHE 0.042 0.012 PHE B 84 HIS 0.016 0.004 HIS B 83 Details of bonding type rmsd covalent geometry : bond 0.01347 ( 1573) covalent geometry : angle 1.84418 ( 2123) hydrogen bonds : bond 0.20005 ( 51) hydrogen bonds : angle 10.53642 ( 162) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8799 (mp0) cc_final: 0.8515 (mp0) REVERT: A 67 GLU cc_start: 0.4546 (mm-30) cc_final: 0.3567 (pt0) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.1967 time to fit residues: 14.4094 Evaluate side-chains 48 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 8 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 15 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 1.9990 chunk 4 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 104 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4369 r_free = 0.4369 target = 0.171262 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.141157 restraints weight = 7107.394| |-----------------------------------------------------------------------------| r_work (start): 0.4033 rms_B_bonded: 4.63 r_work: 0.3909 rms_B_bonded: 4.62 restraints_weight: 0.5000 r_work (final): 0.3909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.4562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 1573 Z= 0.131 Angle : 0.632 4.526 2123 Z= 0.329 Chirality : 0.049 0.171 240 Planarity : 0.004 0.028 280 Dihedral : 4.085 14.725 212 Min Nonbonded Distance : 2.407 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 2.87 % Allowed : 13.22 % Favored : 83.91 % 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 aren not related in a simple way. whole: -2.03 (0.61), residues: 185 helix: None (None), residues: 0 sheet: -1.29 (0.50), residues: 95 loop : -1.27 (0.67), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.006 0.002 TYR B 122 PHE 0.017 0.002 PHE A 75 HIS 0.005 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 1573) covalent geometry : angle 0.63241 ( 2123) hydrogen bonds : bond 0.03430 ( 51) hydrogen bonds : angle 6.51171 ( 162) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 53 time to evaluate : 0.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8902 (mp0) cc_final: 0.8560 (mp0) REVERT: A 67 GLU cc_start: 0.4600 (mm-30) cc_final: 0.3622 (pt0) REVERT: A 132 THR cc_start: 0.8265 (t) cc_final: 0.8006 (p) outliers start: 5 outliers final: 5 residues processed: 55 average time/residue: 0.1733 time to fit residues: 10.4184 Evaluate side-chains 53 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.107 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Chi-restraints excluded: chain A residue 139 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 9 optimal weight: 1.9990 chunk 3 optimal weight: 0.0770 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 11 optimal weight: 3.9990 chunk 16 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 chunk 2 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 overall best weight: 0.6540 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** 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 = 0.4354 r_free = 0.4354 target = 0.169514 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.139924 restraints weight = 7314.070| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 4.63 r_work: 0.3895 rms_B_bonded: 4.58 restraints_weight: 0.5000 r_work (final): 0.3895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6617 moved from start: 0.5273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.016 1573 Z= 0.104 Angle : 0.546 3.966 2123 Z= 0.283 Chirality : 0.048 0.160 240 Planarity : 0.004 0.032 280 Dihedral : 3.863 12.422 212 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.15 % Allowed : 18.97 % Favored : 79.89 % 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 aren not related in a simple way. whole: -1.28 (0.66), residues: 185 helix: None (None), residues: 0 sheet: -0.85 (0.51), residues: 101 loop : -0.64 (0.79), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 74 TYR 0.006 0.002 TYR B 122 PHE 0.010 0.002 PHE A 75 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00237 ( 1573) covalent geometry : angle 0.54582 ( 2123) hydrogen bonds : bond 0.02761 ( 51) hydrogen bonds : angle 5.33987 ( 162) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 50 time to evaluate : 0.052 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 HIS cc_start: 0.6975 (OUTLIER) cc_final: 0.6708 (t-90) REVERT: B 110 GLU cc_start: 0.8924 (mp0) cc_final: 0.8561 (mp0) REVERT: A 67 GLU cc_start: 0.4786 (mm-30) cc_final: 0.3709 (pt0) REVERT: A 132 THR cc_start: 0.8211 (t) cc_final: 0.7917 (p) outliers start: 2 outliers final: 1 residues processed: 52 average time/residue: 0.1308 time to fit residues: 7.6127 Evaluate side-chains 46 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 44 time to evaluate : 0.055 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain A residue 113 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 0.5980 chunk 6 optimal weight: 0.5980 chunk 10 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 1 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 3 optimal weight: 0.0010 chunk 8 optimal weight: 8.9990 overall best weight: 0.6186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 108 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4355 r_free = 0.4355 target = 0.169309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4027 r_free = 0.4027 target = 0.139503 restraints weight = 7130.154| |-----------------------------------------------------------------------------| r_work (start): 0.4015 rms_B_bonded: 4.67 r_work: 0.3882 rms_B_bonded: 4.68 restraints_weight: 0.5000 r_work (final): 0.3882 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6640 moved from start: 0.5640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.015 1573 Z= 0.090 Angle : 0.515 3.851 2123 Z= 0.263 Chirality : 0.048 0.155 240 Planarity : 0.004 0.029 280 Dihedral : 3.791 12.622 212 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 5.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 2.87 % Allowed : 16.67 % Favored : 80.46 % 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 aren not related in a simple way. whole: -0.89 (0.68), residues: 185 helix: None (None), residues: 0 sheet: -0.62 (0.52), residues: 101 loop : -0.34 (0.82), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 74 TYR 0.005 0.002 TYR B 122 PHE 0.011 0.002 PHE A 75 HIS 0.006 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00206 ( 1573) covalent geometry : angle 0.51504 ( 2123) hydrogen bonds : bond 0.02520 ( 51) hydrogen bonds : angle 4.84168 ( 162) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 45 time to evaluate : 0.086 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 HIS cc_start: 0.6933 (OUTLIER) cc_final: 0.6677 (t-90) REVERT: B 110 GLU cc_start: 0.8964 (mp0) cc_final: 0.8611 (mp0) REVERT: B 156 GLU cc_start: 0.7749 (mp0) cc_final: 0.7150 (mp0) REVERT: A 80 ASP cc_start: 0.5991 (p0) cc_final: 0.5622 (p0) REVERT: A 132 THR cc_start: 0.8220 (t) cc_final: 0.7941 (p) outliers start: 5 outliers final: 4 residues processed: 49 average time/residue: 0.1431 time to fit residues: 7.8142 Evaluate side-chains 48 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 43 time to evaluate : 0.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 2.9990 chunk 16 optimal weight: 4.9990 chunk 13 optimal weight: 0.8980 chunk 15 optimal weight: 4.9990 chunk 4 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 10 optimal weight: 0.6980 chunk 11 optimal weight: 0.9990 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** 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 = 0.4328 r_free = 0.4328 target = 0.166815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.136034 restraints weight = 7173.818| |-----------------------------------------------------------------------------| r_work (start): 0.3976 rms_B_bonded: 4.75 r_work: 0.3848 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6716 moved from start: 0.6246 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1573 Z= 0.093 Angle : 0.498 3.713 2123 Z= 0.254 Chirality : 0.047 0.156 240 Planarity : 0.004 0.027 280 Dihedral : 3.675 13.604 212 Min Nonbonded Distance : 2.453 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.45 % Allowed : 17.24 % Favored : 79.31 % 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 aren not related in a simple way. whole: -0.78 (0.68), residues: 185 helix: None (None), residues: 0 sheet: -0.52 (0.53), residues: 101 loop : -0.31 (0.81), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 74 TYR 0.005 0.002 TYR B 122 PHE 0.012 0.002 PHE A 75 HIS 0.007 0.001 HIS A 111 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 1573) covalent geometry : angle 0.49848 ( 2123) hydrogen bonds : bond 0.02337 ( 51) hydrogen bonds : angle 4.58822 ( 162) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 48 time to evaluate : 0.102 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.8993 (mp0) cc_final: 0.8651 (mp0) REVERT: B 156 GLU cc_start: 0.7816 (mp0) cc_final: 0.7169 (mp0) REVERT: A 132 THR cc_start: 0.8277 (t) cc_final: 0.7896 (p) outliers start: 6 outliers final: 6 residues processed: 52 average time/residue: 0.1464 time to fit residues: 8.4359 Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 16 optimal weight: 5.9990 chunk 17 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 3 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 0.2980 chunk 11 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 8 optimal weight: 8.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** 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 = 0.4316 r_free = 0.4316 target = 0.165487 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.135087 restraints weight = 7186.878| |-----------------------------------------------------------------------------| r_work (start): 0.3971 rms_B_bonded: 4.67 r_work: 0.3844 rms_B_bonded: 4.53 restraints_weight: 0.5000 r_work (final): 0.3844 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.6474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1573 Z= 0.092 Angle : 0.491 3.689 2123 Z= 0.251 Chirality : 0.047 0.153 240 Planarity : 0.004 0.027 280 Dihedral : 3.642 13.196 212 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.45 % Allowed : 19.54 % Favored : 77.01 % 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 aren not related in a simple way. whole: -0.68 (0.68), residues: 185 helix: None (None), residues: 0 sheet: -0.44 (0.52), residues: 101 loop : -0.27 (0.81), residues: 84 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 74 TYR 0.005 0.001 TYR B 122 PHE 0.012 0.002 PHE A 75 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00211 ( 1573) covalent geometry : angle 0.49087 ( 2123) hydrogen bonds : bond 0.02308 ( 51) hydrogen bonds : angle 4.44555 ( 162) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.053 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 HIS cc_start: 0.7223 (OUTLIER) cc_final: 0.6751 (t-90) REVERT: B 110 GLU cc_start: 0.8995 (mp0) cc_final: 0.8655 (mp0) REVERT: B 156 GLU cc_start: 0.7831 (mp0) cc_final: 0.7165 (mp0) REVERT: A 68 MET cc_start: 0.7379 (mtt) cc_final: 0.6950 (mtp) REVERT: A 132 THR cc_start: 0.8271 (t) cc_final: 0.7962 (p) outliers start: 6 outliers final: 5 residues processed: 50 average time/residue: 0.1437 time to fit residues: 7.9763 Evaluate side-chains 50 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 10.0000 chunk 2 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 7 optimal weight: 0.9980 chunk 11 optimal weight: 0.0870 chunk 14 optimal weight: 0.9980 chunk 1 optimal weight: 0.9990 chunk 12 optimal weight: 1.9990 chunk 13 optimal weight: 0.9990 overall best weight: 0.6958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** 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 = 0.4317 r_free = 0.4317 target = 0.165363 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3968 r_free = 0.3968 target = 0.134870 restraints weight = 7257.886| |-----------------------------------------------------------------------------| r_work (start): 0.3961 rms_B_bonded: 4.77 r_work: 0.3836 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6745 moved from start: 0.6737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1573 Z= 0.088 Angle : 0.487 3.663 2123 Z= 0.249 Chirality : 0.047 0.154 240 Planarity : 0.003 0.027 280 Dihedral : 3.605 13.126 212 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.45 % Allowed : 20.11 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.66 (0.65), residues: 185 helix: None (None), residues: 0 sheet: -0.31 (0.53), residues: 99 loop : -0.43 (0.75), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 74 TYR 0.006 0.001 TYR B 122 PHE 0.011 0.002 PHE A 75 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00198 ( 1573) covalent geometry : angle 0.48652 ( 2123) hydrogen bonds : bond 0.02259 ( 51) hydrogen bonds : angle 4.34437 ( 162) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.087 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 HIS cc_start: 0.7455 (OUTLIER) cc_final: 0.6696 (t-90) REVERT: B 110 GLU cc_start: 0.9019 (mp0) cc_final: 0.8679 (mp0) REVERT: B 156 GLU cc_start: 0.7828 (mp0) cc_final: 0.7154 (mp0) REVERT: A 68 MET cc_start: 0.7388 (mtt) cc_final: 0.6934 (mtp) REVERT: A 132 THR cc_start: 0.8264 (t) cc_final: 0.7958 (p) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.1253 time to fit residues: 6.8439 Evaluate side-chains 50 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.061 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 17 optimal weight: 0.0980 chunk 3 optimal weight: 0.0970 chunk 13 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 7 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 8.9990 chunk 6 optimal weight: 4.9990 chunk 14 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 0 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** 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 = 0.4315 r_free = 0.4315 target = 0.165126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.134827 restraints weight = 7365.852| |-----------------------------------------------------------------------------| r_work (start): 0.3962 rms_B_bonded: 4.79 r_work: 0.3836 rms_B_bonded: 4.60 restraints_weight: 0.5000 r_work (final): 0.3836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6744 moved from start: 0.6913 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.013 1573 Z= 0.082 Angle : 0.484 3.641 2123 Z= 0.247 Chirality : 0.047 0.149 240 Planarity : 0.003 0.028 280 Dihedral : 3.559 12.324 212 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 4.02 % Allowed : 20.11 % Favored : 75.86 % 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 aren not related in a simple way. whole: -0.57 (0.65), residues: 185 helix: None (None), residues: 0 sheet: -0.22 (0.52), residues: 99 loop : -0.43 (0.76), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 74 TYR 0.005 0.001 TYR B 122 PHE 0.011 0.002 PHE A 75 HIS 0.004 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00189 ( 1573) covalent geometry : angle 0.48373 ( 2123) hydrogen bonds : bond 0.02204 ( 51) hydrogen bonds : angle 4.21903 ( 162) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 46 time to evaluate : 0.077 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 HIS cc_start: 0.7435 (OUTLIER) cc_final: 0.6656 (t-90) REVERT: B 110 GLU cc_start: 0.9017 (mp0) cc_final: 0.8672 (mp0) REVERT: B 156 GLU cc_start: 0.7837 (mp0) cc_final: 0.7152 (mp0) REVERT: A 68 MET cc_start: 0.7395 (mtt) cc_final: 0.6976 (mtp) REVERT: A 132 THR cc_start: 0.8230 (t) cc_final: 0.7931 (p) outliers start: 7 outliers final: 5 residues processed: 51 average time/residue: 0.1429 time to fit residues: 8.1014 Evaluate side-chains 51 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 1 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 17 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 chunk 3 optimal weight: 1.9990 chunk 5 optimal weight: 0.0980 chunk 4 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** 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 = 0.4296 r_free = 0.4296 target = 0.163578 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.133141 restraints weight = 7481.127| |-----------------------------------------------------------------------------| r_work (start): 0.3943 rms_B_bonded: 4.82 r_work: 0.3816 rms_B_bonded: 4.63 restraints_weight: 0.5000 r_work (final): 0.3816 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6814 moved from start: 0.7252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1573 Z= 0.096 Angle : 0.502 3.613 2123 Z= 0.259 Chirality : 0.048 0.157 240 Planarity : 0.004 0.027 280 Dihedral : 3.622 12.383 212 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.45 % Allowed : 21.26 % Favored : 75.29 % 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 aren not related in a simple way. whole: -0.52 (0.65), residues: 185 helix: None (None), residues: 0 sheet: 0.05 (0.54), residues: 93 loop : -0.68 (0.73), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 116 TYR 0.006 0.002 TYR B 122 PHE 0.013 0.002 PHE A 75 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 1573) covalent geometry : angle 0.50162 ( 2123) hydrogen bonds : bond 0.02180 ( 51) hydrogen bonds : angle 4.33101 ( 162) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 110 GLU cc_start: 0.9004 (mp0) cc_final: 0.8660 (mp0) REVERT: B 156 GLU cc_start: 0.7885 (mp0) cc_final: 0.7196 (mp0) REVERT: A 68 MET cc_start: 0.7483 (mtt) cc_final: 0.7070 (mtp) REVERT: A 132 THR cc_start: 0.8265 (t) cc_final: 0.7948 (p) outliers start: 6 outliers final: 6 residues processed: 50 average time/residue: 0.1427 time to fit residues: 7.9457 Evaluate side-chains 50 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 44 time to evaluate : 0.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 8 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 7 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 5 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 11 optimal weight: 0.0050 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** 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 = 0.4314 r_free = 0.4314 target = 0.165481 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3966 r_free = 0.3966 target = 0.134999 restraints weight = 7268.951| |-----------------------------------------------------------------------------| r_work (start): 0.3956 rms_B_bonded: 4.74 r_work: 0.3830 rms_B_bonded: 4.61 restraints_weight: 0.5000 r_work (final): 0.3830 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.7368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 1573 Z= 0.083 Angle : 0.484 3.636 2123 Z= 0.248 Chirality : 0.047 0.152 240 Planarity : 0.005 0.059 280 Dihedral : 3.535 12.058 212 Min Nonbonded Distance : 2.372 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.24 % Favored : 96.76 % Rotamer: Outliers : 3.45 % Allowed : 20.69 % Favored : 75.86 % 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 aren not related in a simple way. whole: -0.47 (0.65), residues: 185 helix: None (None), residues: 0 sheet: 0.11 (0.54), residues: 93 loop : -0.70 (0.72), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 74 TYR 0.005 0.001 TYR B 122 PHE 0.014 0.002 PHE A 75 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00200 ( 1573) covalent geometry : angle 0.48352 ( 2123) hydrogen bonds : bond 0.02131 ( 51) hydrogen bonds : angle 4.19340 ( 162) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 370 Ramachandran restraints generated. 185 Oldfield, 0 Emsley, 185 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.088 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 104 HIS cc_start: 0.7508 (OUTLIER) cc_final: 0.6669 (t-90) REVERT: B 110 GLU cc_start: 0.9014 (mp0) cc_final: 0.8673 (mp0) REVERT: B 156 GLU cc_start: 0.7923 (mp0) cc_final: 0.7242 (mp0) REVERT: A 68 MET cc_start: 0.7457 (mtt) cc_final: 0.7252 (mtp) REVERT: A 132 THR cc_start: 0.8235 (t) cc_final: 0.7904 (p) outliers start: 6 outliers final: 5 residues processed: 49 average time/residue: 0.1473 time to fit residues: 8.0181 Evaluate side-chains 51 residues out of total 174 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 45 time to evaluate : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 82 LYS Chi-restraints excluded: chain B residue 104 HIS Chi-restraints excluded: chain B residue 129 ASP Chi-restraints excluded: chain A residue 97 VAL Chi-restraints excluded: chain A residue 113 PHE Chi-restraints excluded: chain A residue 135 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 18 random chunks: chunk 4 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 11 optimal weight: 0.0270 chunk 15 optimal weight: 4.9990 chunk 16 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 14 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 1 optimal weight: 0.8980 overall best weight: 0.6438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 101 HIS ** 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 = 0.4305 r_free = 0.4305 target = 0.164378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3957 r_free = 0.3957 target = 0.134034 restraints weight = 7339.385| |-----------------------------------------------------------------------------| r_work (start): 0.3950 rms_B_bonded: 4.76 r_work: 0.3827 rms_B_bonded: 4.59 restraints_weight: 0.5000 r_work (final): 0.3827 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6808 moved from start: 0.7509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 1573 Z= 0.084 Angle : 0.481 3.616 2123 Z= 0.245 Chirality : 0.047 0.151 240 Planarity : 0.004 0.046 280 Dihedral : 3.456 11.830 212 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.45 % Allowed : 20.69 % Favored : 75.86 % 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 aren not related in a simple way. whole: -0.49 (0.65), residues: 185 helix: None (None), residues: 0 sheet: 0.08 (0.55), residues: 94 loop : -0.68 (0.72), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 116 TYR 0.005 0.001 TYR B 122 PHE 0.015 0.002 PHE A 75 HIS 0.003 0.001 HIS B 119 Details of bonding type rmsd covalent geometry : bond 0.00197 ( 1573) covalent geometry : angle 0.48084 ( 2123) hydrogen bonds : bond 0.02056 ( 51) hydrogen bonds : angle 4.09949 ( 162) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1555.71 seconds wall clock time: 27 minutes 3.34 seconds (1623.34 seconds total)