Starting phenix.real_space_refine on Thu Jul 18 22:12:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/07_2024/8hfc_34717_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/07_2024/8hfc_34717.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/07_2024/8hfc_34717.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/07_2024/8hfc_34717.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/07_2024/8hfc_34717_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8hfc_34717/07_2024/8hfc_34717_neut.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.004 sd= 0.145 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 Zn 2 6.06 5 S 22 5.16 5 C 2590 2.51 5 N 694 2.21 5 O 699 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 145": "NH1" <-> "NH2" Residue "A GLU 153": "OE1" <-> "OE2" Residue "A ARG 242": "NH1" <-> "NH2" Residue "A GLU 243": "OE1" <-> "OE2" Residue "A GLU 305": "OE1" <-> "OE2" Residue "A GLU 306": "OE1" <-> "OE2" Residue "B GLU 25": "OE1" <-> "OE2" Residue "B GLU 32": "OE1" <-> "OE2" Residue "B GLU 37": "OE1" <-> "OE2" Residue "B GLU 81": "OE1" <-> "OE2" Residue "B GLU 87": "OE1" <-> "OE2" Residue "B GLU 143": "OE1" <-> "OE2" Residue "B ARG 147": "NH1" <-> "NH2" Residue "B GLU 213": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 4007 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2234 Number of conformers: 1 Conformer: "" Number of residues, atoms: 276, 2234 Classifications: {'peptide': 276} Link IDs: {'PTRANS': 16, 'TRANS': 259} Chain: "B" Number of atoms: 1756 Number of conformers: 1 Conformer: "" Number of residues, atoms: 222, 1756 Classifications: {'peptide': 222} Link IDs: {'PTRANS': 13, 'TRANS': 208} Chain: "A" Number of atoms: 17 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 17 Unusual residues: {' ZN': 2, 'PLM': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'PLM:plan-1': 1} Unresolved non-hydrogen planarities: 1 List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 953 SG CYS A 189 39.293 32.069 58.239 1.00 43.49 S ATOM 972 SG CYS A 192 39.223 35.988 57.314 1.00 49.55 S ATOM 1110 SG CYS A 209 36.468 33.802 57.411 1.00 32.51 S ATOM 837 SG CYS A 175 39.498 31.365 69.663 1.00 35.51 S ATOM 856 SG CYS A 178 38.830 35.231 68.292 1.00 36.69 S ATOM 993 SG CYS A 195 36.831 32.303 67.459 1.00 31.03 S Time building chain proxies: 3.17, per 1000 atoms: 0.79 Number of scatterers: 4007 At special positions: 0 Unit cell: (60.872, 65.22, 117.396, 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) Zn 2 29.99 S 22 16.00 O 699 8.00 N 694 7.00 C 2590 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 114 " - pdb=" SG CYS B 126 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.54 Conformation dependent library (CDL) restraints added in 670.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 402 " pdb="ZN ZN A 402 " - pdb=" ND1 HIS A 202 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 209 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 189 " pdb="ZN ZN A 402 " - pdb=" SG CYS A 192 " pdb=" ZN A 403 " pdb="ZN ZN A 403 " - pdb=" ND1 HIS A 188 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 175 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 178 " pdb="ZN ZN A 403 " - pdb=" SG CYS A 195 " Number of angles added : 6 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 928 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 7 sheets defined 41.2% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 76 through 94 removed outlier: 3.807A pdb=" N VAL A 80 " --> pdb=" O LEU A 76 " (cutoff:3.500A) Proline residue: A 87 - end of helix removed outlier: 3.874A pdb=" N PHE A 94 " --> pdb=" O LEU A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 129 Processing helix chain 'A' and resid 214 through 243 Processing helix chain 'A' and resid 246 through 249 Processing helix chain 'A' and resid 250 through 264 removed outlier: 4.000A pdb=" N ILE A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 264 through 279 removed outlier: 3.606A pdb=" N ALA A 268 " --> pdb=" O LEU A 264 " (cutoff:3.500A) Processing helix chain 'A' and resid 283 through 291 Processing helix chain 'A' and resid 313 through 323 Processing helix chain 'B' and resid 45 through 49 Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 130 through 135 Processing helix chain 'B' and resid 137 through 157 Processing helix chain 'B' and resid 161 through 174 Processing helix chain 'B' and resid 188 through 190 No H-bonds generated for 'chain 'B' and resid 188 through 190' Processing helix chain 'B' and resid 191 through 206 removed outlier: 3.864A pdb=" N LEU B 195 " --> pdb=" O PHE B 191 " (cutoff:3.500A) Processing helix chain 'B' and resid 209 through 215 removed outlier: 3.643A pdb=" N ARG B 214 " --> pdb=" O LEU B 210 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 158 through 160 Processing sheet with id=AA2, first strand: chain 'A' and resid 174 through 175 removed outlier: 3.825A pdb=" N ILE A 180 " --> pdb=" O CYS A 175 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 187 through 189 removed outlier: 3.774A pdb=" N VAL A 194 " --> pdb=" O CYS A 189 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 202 through 203 Processing sheet with id=AA5, first strand: chain 'B' and resid 27 through 28 Processing sheet with id=AA6, first strand: chain 'B' and resid 32 through 33 Processing sheet with id=AA7, first strand: chain 'B' and resid 70 through 75 160 hydrogen bonds defined for protein. 435 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: 0.98 Time building geometry restraints manager: 1.69 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1281 1.34 - 1.46: 843 1.46 - 1.58: 1967 1.58 - 1.70: 1 1.70 - 1.82: 29 Bond restraints: 4121 Sorted by residual: bond pdb=" C1 PLM A 401 " pdb=" C2 PLM A 401 " ideal model delta sigma weight residual 1.542 1.599 -0.057 2.00e-02 2.50e+03 8.25e+00 bond pdb=" CA VAL B 233 " pdb=" CB VAL B 233 " ideal model delta sigma weight residual 1.546 1.534 0.012 8.80e-03 1.29e+04 1.95e+00 bond pdb=" C6 PLM A 401 " pdb=" C7 PLM A 401 " ideal model delta sigma weight residual 1.525 1.552 -0.027 2.00e-02 2.50e+03 1.87e+00 bond pdb=" C2 PLM A 401 " pdb=" C3 PLM A 401 " ideal model delta sigma weight residual 1.522 1.549 -0.027 2.00e-02 2.50e+03 1.84e+00 bond pdb=" CB TRP A 117 " pdb=" CG TRP A 117 " ideal model delta sigma weight residual 1.498 1.456 0.042 3.10e-02 1.04e+03 1.84e+00 ... (remaining 4116 not shown) Histogram of bond angle deviations from ideal: 100.06 - 106.85: 156 106.85 - 113.63: 2236 113.63 - 120.42: 1617 120.42 - 127.21: 1517 127.21 - 133.99: 69 Bond angle restraints: 5595 Sorted by residual: angle pdb=" C TYR B 117 " pdb=" N ASP B 118 " pdb=" CA ASP B 118 " ideal model delta sigma weight residual 121.54 128.59 -7.05 1.91e+00 2.74e-01 1.36e+01 angle pdb=" N ILE A 93 " pdb=" CA ILE A 93 " pdb=" C ILE A 93 " ideal model delta sigma weight residual 111.81 108.81 3.00 8.60e-01 1.35e+00 1.22e+01 angle pdb=" C ARG B 116 " pdb=" N TYR B 117 " pdb=" CA TYR B 117 " ideal model delta sigma weight residual 121.54 127.66 -6.12 1.91e+00 2.74e-01 1.03e+01 angle pdb=" C ASP A 341 " pdb=" N TRP A 342 " pdb=" CA TRP A 342 " ideal model delta sigma weight residual 121.54 125.75 -4.21 1.91e+00 2.74e-01 4.86e+00 angle pdb=" N ARG B 188 " pdb=" CA ARG B 188 " pdb=" C ARG B 188 " ideal model delta sigma weight residual 109.81 114.56 -4.75 2.21e+00 2.05e-01 4.61e+00 ... (remaining 5590 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 2036 17.51 - 35.01: 288 35.01 - 52.52: 78 52.52 - 70.03: 16 70.03 - 87.53: 7 Dihedral angle restraints: 2425 sinusoidal: 982 harmonic: 1443 Sorted by residual: dihedral pdb=" CA ARG B 188 " pdb=" C ARG B 188 " pdb=" N PRO B 189 " pdb=" CA PRO B 189 " ideal model delta harmonic sigma weight residual -180.00 -160.89 -19.11 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA GLY B 176 " pdb=" C GLY B 176 " pdb=" N LEU B 177 " pdb=" CA LEU B 177 " ideal model delta harmonic sigma weight residual -180.00 -160.92 -19.08 0 5.00e+00 4.00e-02 1.46e+01 dihedral pdb=" CA LEU B 185 " pdb=" C LEU B 185 " pdb=" N LEU B 186 " pdb=" CA LEU B 186 " ideal model delta harmonic sigma weight residual -180.00 -161.50 -18.50 0 5.00e+00 4.00e-02 1.37e+01 ... (remaining 2422 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 275 0.027 - 0.053: 184 0.053 - 0.079: 92 0.079 - 0.106: 43 0.106 - 0.132: 12 Chirality restraints: 606 Sorted by residual: chirality pdb=" CA VAL B 233 " pdb=" N VAL B 233 " pdb=" C VAL B 233 " pdb=" CB VAL B 233 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 chirality pdb=" CA VAL B 216 " pdb=" N VAL B 216 " pdb=" C VAL B 216 " pdb=" CB VAL B 216 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA PRO A 267 " pdb=" N PRO A 267 " pdb=" C PRO A 267 " pdb=" CB PRO A 267 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 603 not shown) Planarity restraints: 713 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR A 266 " 0.032 5.00e-02 4.00e+02 4.78e-02 3.65e+00 pdb=" N PRO A 267 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 267 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 267 " 0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 88 " 0.023 5.00e-02 4.00e+02 3.53e-02 2.00e+00 pdb=" N PRO B 89 " -0.061 5.00e-02 4.00e+02 pdb=" CA PRO B 89 " 0.018 5.00e-02 4.00e+02 pdb=" CD PRO B 89 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE B 55 " 0.019 5.00e-02 4.00e+02 2.85e-02 1.30e+00 pdb=" N PRO B 56 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO B 56 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO B 56 " 0.016 5.00e-02 4.00e+02 ... (remaining 710 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 186 2.71 - 3.26: 3917 3.26 - 3.81: 6278 3.81 - 4.35: 7274 4.35 - 4.90: 13142 Nonbonded interactions: 30797 Sorted by model distance: nonbonded pdb=" O SER B 224 " pdb=" OG SER B 224 " model vdw 2.164 2.440 nonbonded pdb=" OH TYR B 59 " pdb=" OD2 ASP B 230 " model vdw 2.203 2.440 nonbonded pdb=" O TYR B 135 " pdb=" NH1 ARG B 214 " model vdw 2.203 2.520 nonbonded pdb=" O ALA A 83 " pdb=" OH TYR A 259 " model vdw 2.211 2.440 nonbonded pdb=" OE2 GLU B 155 " pdb=" OG SER B 194 " model vdw 2.238 2.440 ... (remaining 30792 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.310 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.890 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.010 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.069 4121 Z= 0.451 Angle : 0.671 7.046 5595 Z= 0.372 Chirality : 0.046 0.132 606 Planarity : 0.004 0.048 713 Dihedral : 18.011 87.532 1494 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 9.17 Ramachandran Plot: Outliers : 0.20 % Allowed : 6.48 % Favored : 93.32 % Rotamer: Outliers : 3.88 % Allowed : 24.20 % Favored : 71.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.90 (0.33), residues: 494 helix: -0.85 (0.34), residues: 175 sheet: -2.79 (0.61), residues: 40 loop : -2.60 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 162 HIS 0.003 0.001 HIS A 202 PHE 0.013 0.002 PHE A 218 TYR 0.011 0.002 TYR B 117 ARG 0.003 0.000 ARG B 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.443 Fit side-chains REVERT: A 153 GLU cc_start: 0.8224 (mp0) cc_final: 0.7935 (mp0) REVERT: B 116 ARG cc_start: 0.7613 (mtm-85) cc_final: 0.7324 (mmm-85) REVERT: B 222 ARG cc_start: 0.8421 (tmt170) cc_final: 0.8093 (tmt170) outliers start: 17 outliers final: 12 residues processed: 82 average time/residue: 0.1675 time to fit residues: 17.0546 Evaluate side-chains 70 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 58 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 86 CYS Chi-restraints excluded: chain A residue 120 THR Chi-restraints excluded: chain A residue 123 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 192 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 126 CYS Chi-restraints excluded: chain B residue 166 SER Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.9990 chunk 37 optimal weight: 7.9990 chunk 20 optimal weight: 0.9990 chunk 12 optimal weight: 0.6980 chunk 25 optimal weight: 0.0670 chunk 19 optimal weight: 0.9980 chunk 38 optimal weight: 0.0870 chunk 14 optimal weight: 0.5980 chunk 23 optimal weight: 0.0670 chunk 28 optimal weight: 0.7980 chunk 44 optimal weight: 3.9990 overall best weight: 0.3034 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 199 HIS A 282 GLN A 296 ASN A 300 HIS A 307 ASN A 320 HIS ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 4121 Z= 0.125 Angle : 0.508 6.295 5595 Z= 0.262 Chirality : 0.040 0.135 606 Planarity : 0.004 0.031 713 Dihedral : 6.631 56.373 575 Min Nonbonded Distance : 2.198 Molprobity Statistics. All-atom Clashscore : 5.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer: Outliers : 3.88 % Allowed : 24.89 % Favored : 71.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.09 (0.37), residues: 494 helix: 0.83 (0.37), residues: 190 sheet: -1.29 (0.76), residues: 34 loop : -1.88 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 178 HIS 0.004 0.001 HIS B 212 PHE 0.009 0.001 PHE B 231 TYR 0.016 0.001 TYR B 200 ARG 0.002 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.444 Fit side-chains REVERT: A 88 MET cc_start: 0.7354 (tmm) cc_final: 0.7117 (tmm) REVERT: A 153 GLU cc_start: 0.8199 (mp0) cc_final: 0.7891 (mp0) REVERT: A 239 HIS cc_start: 0.8320 (t-170) cc_final: 0.7865 (t-170) REVERT: A 291 ILE cc_start: 0.6107 (OUTLIER) cc_final: 0.5762 (tt) REVERT: B 222 ARG cc_start: 0.8414 (tmt170) cc_final: 0.8190 (tmt170) outliers start: 17 outliers final: 7 residues processed: 88 average time/residue: 0.1517 time to fit residues: 16.8430 Evaluate side-chains 72 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 64 time to evaluate : 0.442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 273 TYR Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 104 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 37 optimal weight: 8.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.9980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7898 moved from start: 0.1415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 4121 Z= 0.287 Angle : 0.576 7.397 5595 Z= 0.290 Chirality : 0.043 0.135 606 Planarity : 0.004 0.033 713 Dihedral : 5.296 41.907 561 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.48 % Favored : 93.52 % Rotamer: Outliers : 5.25 % Allowed : 24.89 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.69 (0.38), residues: 494 helix: 1.24 (0.38), residues: 190 sheet: -1.38 (0.66), residues: 44 loop : -1.66 (0.39), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 178 HIS 0.004 0.001 HIS B 212 PHE 0.011 0.001 PHE A 218 TYR 0.012 0.001 TYR B 200 ARG 0.002 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 72 time to evaluate : 0.440 Fit side-chains REVERT: A 88 MET cc_start: 0.7252 (tmm) cc_final: 0.6985 (tmm) REVERT: A 153 GLU cc_start: 0.8241 (mp0) cc_final: 0.7918 (mp0) REVERT: A 239 HIS cc_start: 0.8468 (t-170) cc_final: 0.8256 (t-170) REVERT: A 291 ILE cc_start: 0.6089 (OUTLIER) cc_final: 0.5799 (tt) REVERT: B 94 GLN cc_start: 0.8728 (mt0) cc_final: 0.8461 (tt0) REVERT: B 116 ARG cc_start: 0.7949 (mmm-85) cc_final: 0.7454 (mmm-85) REVERT: B 218 LEU cc_start: 0.8829 (OUTLIER) cc_final: 0.8618 (tt) outliers start: 23 outliers final: 15 residues processed: 89 average time/residue: 0.1625 time to fit residues: 18.0660 Evaluate side-chains 81 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 64 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 262 LEU Chi-restraints excluded: chain A residue 291 ILE Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 218 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.0030 chunk 4 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 29 optimal weight: 0.2980 chunk 44 optimal weight: 0.0020 chunk 47 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4121 Z= 0.132 Angle : 0.505 6.039 5595 Z= 0.254 Chirality : 0.040 0.136 606 Planarity : 0.004 0.031 713 Dihedral : 4.628 34.296 561 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 6.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.88 % Allowed : 25.11 % Favored : 71.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.01 (0.39), residues: 494 helix: 1.86 (0.39), residues: 184 sheet: -0.67 (0.75), residues: 34 loop : -1.29 (0.39), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 100 HIS 0.005 0.001 HIS B 212 PHE 0.009 0.001 PHE A 287 TYR 0.009 0.001 TYR B 59 ARG 0.001 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 71 time to evaluate : 0.432 Fit side-chains REVERT: A 88 MET cc_start: 0.7191 (tmm) cc_final: 0.6921 (tmm) REVERT: A 153 GLU cc_start: 0.8203 (mp0) cc_final: 0.7879 (mp0) REVERT: A 321 LEU cc_start: 0.8861 (OUTLIER) cc_final: 0.8626 (tm) REVERT: B 94 GLN cc_start: 0.8698 (mt0) cc_final: 0.8443 (tt0) REVERT: B 116 ARG cc_start: 0.8109 (mmm-85) cc_final: 0.7734 (mmm-85) REVERT: B 205 ASN cc_start: 0.7637 (m-40) cc_final: 0.7430 (m-40) outliers start: 17 outliers final: 10 residues processed: 84 average time/residue: 0.1367 time to fit residues: 14.7778 Evaluate side-chains 76 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 65 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 243 GLU Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 3.9990 chunk 19 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 42 optimal weight: 0.0980 chunk 11 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4121 Z= 0.176 Angle : 0.535 8.746 5595 Z= 0.261 Chirality : 0.041 0.124 606 Planarity : 0.004 0.031 713 Dihedral : 4.611 33.328 561 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.57 % Allowed : 25.80 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.39), residues: 494 helix: 1.96 (0.39), residues: 184 sheet: -0.55 (0.75), residues: 34 loop : -1.21 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.009 0.001 HIS A 239 PHE 0.009 0.001 PHE A 287 TYR 0.009 0.001 TYR A 115 ARG 0.002 0.000 ARG A 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 61 time to evaluate : 0.580 Fit side-chains REVERT: A 88 MET cc_start: 0.7157 (tmm) cc_final: 0.6845 (tmm) REVERT: A 153 GLU cc_start: 0.8191 (mp0) cc_final: 0.7918 (mp0) REVERT: B 94 GLN cc_start: 0.8704 (mt0) cc_final: 0.8447 (tt0) REVERT: B 116 ARG cc_start: 0.8178 (mmm-85) cc_final: 0.7759 (mmm-85) REVERT: B 205 ASN cc_start: 0.7819 (m-40) cc_final: 0.7570 (m110) outliers start: 20 outliers final: 16 residues processed: 75 average time/residue: 0.1443 time to fit residues: 13.8470 Evaluate side-chains 79 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 21 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 5 optimal weight: 0.0050 chunk 27 optimal weight: 5.9990 chunk 34 optimal weight: 0.0370 overall best weight: 0.4072 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 68 GLN ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7805 moved from start: 0.2300 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 4121 Z= 0.132 Angle : 0.523 7.860 5595 Z= 0.255 Chirality : 0.040 0.141 606 Planarity : 0.004 0.032 713 Dihedral : 4.477 33.095 561 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.86 % Favored : 95.14 % Rotamer: Outliers : 3.88 % Allowed : 26.26 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.39), residues: 494 helix: 2.16 (0.38), residues: 183 sheet: -0.48 (0.75), residues: 34 loop : -1.14 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 100 HIS 0.009 0.001 HIS A 239 PHE 0.009 0.001 PHE A 287 TYR 0.010 0.001 TYR A 115 ARG 0.002 0.000 ARG B 113 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 65 time to evaluate : 0.453 Fit side-chains REVERT: A 88 MET cc_start: 0.7118 (tmm) cc_final: 0.6840 (tmm) REVERT: A 103 GLN cc_start: 0.7378 (pm20) cc_final: 0.6940 (pm20) REVERT: A 153 GLU cc_start: 0.8201 (mp0) cc_final: 0.7853 (mp0) REVERT: A 321 LEU cc_start: 0.8949 (OUTLIER) cc_final: 0.8734 (tm) REVERT: B 94 GLN cc_start: 0.8706 (mt0) cc_final: 0.8455 (tt0) REVERT: B 116 ARG cc_start: 0.8080 (mmm-85) cc_final: 0.7751 (tpp80) REVERT: B 205 ASN cc_start: 0.7718 (m-40) cc_final: 0.7455 (m-40) outliers start: 17 outliers final: 12 residues processed: 76 average time/residue: 0.1356 time to fit residues: 13.3087 Evaluate side-chains 74 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 61 time to evaluate : 0.433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 0.6980 chunk 47 optimal weight: 0.8980 chunk 29 optimal weight: 2.9990 chunk 28 optimal weight: 10.0000 chunk 21 optimal weight: 0.0870 chunk 18 optimal weight: 2.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.9362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7853 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4121 Z= 0.210 Angle : 0.550 9.099 5595 Z= 0.267 Chirality : 0.041 0.135 606 Planarity : 0.004 0.032 713 Dihedral : 4.593 33.547 561 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 4.34 % Allowed : 25.34 % Favored : 70.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.39), residues: 494 helix: 2.09 (0.38), residues: 184 sheet: -0.39 (0.76), residues: 34 loop : -1.16 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 178 HIS 0.008 0.001 HIS A 239 PHE 0.009 0.001 PHE A 287 TYR 0.015 0.001 TYR B 200 ARG 0.001 0.000 ARG A 126 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 61 time to evaluate : 0.441 Fit side-chains REVERT: A 88 MET cc_start: 0.7129 (tmm) cc_final: 0.6806 (tmm) REVERT: B 94 GLN cc_start: 0.8717 (mt0) cc_final: 0.8467 (tt0) REVERT: B 205 ASN cc_start: 0.7799 (m-40) cc_final: 0.7552 (m-40) outliers start: 19 outliers final: 17 residues processed: 76 average time/residue: 0.1463 time to fit residues: 14.2652 Evaluate side-chains 76 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 LEU Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 130 SER Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 37 optimal weight: 6.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.0570 chunk 13 optimal weight: 0.9990 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.2329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4121 Z= 0.165 Angle : 0.533 9.113 5595 Z= 0.258 Chirality : 0.041 0.156 606 Planarity : 0.004 0.032 713 Dihedral : 4.482 32.838 561 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 3.65 % Allowed : 26.71 % Favored : 69.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.36 (0.39), residues: 494 helix: 2.17 (0.38), residues: 184 sheet: -0.35 (0.76), residues: 34 loop : -1.10 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 178 HIS 0.009 0.001 HIS A 239 PHE 0.009 0.001 PHE A 287 TYR 0.009 0.001 TYR A 115 ARG 0.001 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 63 time to evaluate : 0.440 Fit side-chains REVERT: A 88 MET cc_start: 0.7095 (tmm) cc_final: 0.6818 (tmm) REVERT: B 94 GLN cc_start: 0.8715 (mt0) cc_final: 0.8460 (tt0) REVERT: B 116 ARG cc_start: 0.8271 (mmm-85) cc_final: 0.7941 (tpp80) REVERT: B 205 ASN cc_start: 0.7771 (m-40) cc_final: 0.7531 (m-40) outliers start: 16 outliers final: 15 residues processed: 75 average time/residue: 0.1423 time to fit residues: 13.6366 Evaluate side-chains 75 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 60 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 28 optimal weight: 0.6980 chunk 46 optimal weight: 0.9980 chunk 22 optimal weight: 10.0000 chunk 32 optimal weight: 2.9990 chunk 48 optimal weight: 0.5980 chunk 44 optimal weight: 0.7980 chunk 38 optimal weight: 0.0020 chunk 4 optimal weight: 0.6980 overall best weight: 0.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.2509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 4121 Z= 0.156 Angle : 0.537 9.303 5595 Z= 0.258 Chirality : 0.040 0.154 606 Planarity : 0.004 0.033 713 Dihedral : 4.370 32.581 561 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 6.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.47 % Favored : 94.53 % Rotamer: Outliers : 3.20 % Allowed : 26.94 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.44 (0.39), residues: 494 helix: 2.26 (0.38), residues: 184 sheet: -0.37 (0.77), residues: 34 loop : -1.06 (0.38), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 178 HIS 0.009 0.001 HIS A 239 PHE 0.009 0.001 PHE A 287 TYR 0.017 0.001 TYR B 200 ARG 0.002 0.000 ARG B 116 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 62 time to evaluate : 0.446 Fit side-chains REVERT: A 88 MET cc_start: 0.7183 (tmm) cc_final: 0.6904 (tmm) REVERT: A 153 GLU cc_start: 0.8107 (mp0) cc_final: 0.7820 (mp0) REVERT: A 168 LYS cc_start: 0.7834 (mmmt) cc_final: 0.7196 (mtmt) REVERT: B 94 GLN cc_start: 0.8713 (mt0) cc_final: 0.8461 (tt0) REVERT: B 116 ARG cc_start: 0.8229 (mmm-85) cc_final: 0.7973 (tpp80) outliers start: 14 outliers final: 14 residues processed: 72 average time/residue: 0.1500 time to fit residues: 13.8392 Evaluate side-chains 77 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 166 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 2.9990 chunk 23 optimal weight: 5.9990 chunk 41 optimal weight: 0.5980 chunk 11 optimal weight: 0.8980 chunk 35 optimal weight: 5.9990 chunk 5 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 16 optimal weight: 0.0770 chunk 39 optimal weight: 0.7980 chunk 4 optimal weight: 0.5980 overall best weight: 0.3896 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7794 moved from start: 0.2642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 4121 Z= 0.139 Angle : 0.529 8.806 5595 Z= 0.254 Chirality : 0.040 0.154 606 Planarity : 0.004 0.033 713 Dihedral : 4.234 32.361 561 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 3.20 % Allowed : 26.71 % Favored : 70.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.39), residues: 494 helix: 2.41 (0.39), residues: 183 sheet: -0.32 (0.76), residues: 34 loop : -1.03 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.011 0.001 HIS A 239 PHE 0.009 0.001 PHE A 287 TYR 0.009 0.001 TYR A 115 ARG 0.002 0.000 ARG B 116 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 988 Ramachandran restraints generated. 494 Oldfield, 0 Emsley, 494 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 67 time to evaluate : 0.434 Fit side-chains REVERT: A 88 MET cc_start: 0.7189 (tmm) cc_final: 0.6913 (tmm) REVERT: A 153 GLU cc_start: 0.8084 (mp0) cc_final: 0.7773 (mp0) REVERT: A 168 LYS cc_start: 0.7837 (mmmt) cc_final: 0.7203 (mtmt) REVERT: B 94 GLN cc_start: 0.8710 (mt0) cc_final: 0.8465 (tt0) outliers start: 14 outliers final: 14 residues processed: 77 average time/residue: 0.1517 time to fit residues: 15.0546 Evaluate side-chains 77 residues out of total 438 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 63 time to evaluate : 0.438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 85 VAL Chi-restraints excluded: chain A residue 108 VAL Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain A residue 172 ILE Chi-restraints excluded: chain A residue 258 CYS Chi-restraints excluded: chain A residue 318 MET Chi-restraints excluded: chain A residue 321 LEU Chi-restraints excluded: chain B residue 25 GLU Chi-restraints excluded: chain B residue 30 PHE Chi-restraints excluded: chain B residue 104 VAL Chi-restraints excluded: chain B residue 118 ASP Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 173 LEU Chi-restraints excluded: chain B residue 232 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.0070 chunk 34 optimal weight: 0.9990 chunk 2 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 44 optimal weight: 0.0050 chunk 26 optimal weight: 0.1980 chunk 33 optimal weight: 0.0870 chunk 1 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 10.0000 chunk 19 optimal weight: 0.8980 overall best weight: 0.2390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 24 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 149 ASN ** 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 = 0.3923 r_free = 0.3923 target = 0.176137 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.131976 restraints weight = 4610.513| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.133154 restraints weight = 3982.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3474 r_free = 0.3474 target = 0.133596 restraints weight = 3443.840| |-----------------------------------------------------------------------------| r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 4121 Z= 0.128 Angle : 0.524 9.120 5595 Z= 0.256 Chirality : 0.040 0.151 606 Planarity : 0.004 0.034 713 Dihedral : 4.136 32.224 561 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.25 % Favored : 95.75 % Rotamer: Outliers : 2.51 % Allowed : 27.63 % Favored : 69.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.63 (0.39), residues: 494 helix: 2.49 (0.39), residues: 183 sheet: -0.28 (0.76), residues: 34 loop : -0.99 (0.38), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 178 HIS 0.011 0.001 HIS A 239 PHE 0.010 0.001 PHE A 287 TYR 0.010 0.001 TYR A 115 ARG 0.006 0.000 ARG B 116 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1210.59 seconds wall clock time: 21 minutes 57.24 seconds (1317.24 seconds total)