Starting phenix.real_space_refine on Mon Feb 10 22:43:08 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8qcs_18334/02_2025/8qcs_18334.cif Found real_map, /net/cci-nas-00/data/ceres_data/8qcs_18334/02_2025/8qcs_18334.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8qcs_18334/02_2025/8qcs_18334.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8qcs_18334/02_2025/8qcs_18334.map" model { file = "/net/cci-nas-00/data/ceres_data/8qcs_18334/02_2025/8qcs_18334.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8qcs_18334/02_2025/8qcs_18334.cif" } resolution = 2.9 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= 0.003 sd= 0.097 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2156 2.51 5 N 500 2.21 5 O 567 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 3241 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3241 Number of conformers: 1 Conformer: "" Number of residues, atoms: 417, 3241 Classifications: {'peptide': 417} Link IDs: {'PTRANS': 17, 'TRANS': 399} Time building chain proxies: 2.38, per 1000 atoms: 0.73 Number of scatterers: 3241 At special positions: 0 Unit cell: (80.22, 55.008, 65.322, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 567 8.00 N 500 7.00 C 2156 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.04 Conformation dependent library (CDL) restraints added in 697.1 milliseconds 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 764 Finding SS restraints... Secondary structure from input PDB file: 21 helices and 0 sheets defined 90.4% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 105 through 127 removed outlier: 4.213A pdb=" N VAL A 109 " --> pdb=" O PRO A 105 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE A 126 " --> pdb=" O ALA A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 131 through 140 removed outlier: 4.068A pdb=" N GLY A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.719A pdb=" N ILE A 146 " --> pdb=" O THR A 142 " (cutoff:3.500A) removed outlier: 3.839A pdb=" N SER A 150 " --> pdb=" O ILE A 146 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N TYR A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) removed outlier: 4.384A pdb=" N MET A 154 " --> pdb=" O SER A 150 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 171 removed outlier: 3.722A pdb=" N LEU A 160 " --> pdb=" O ALA A 156 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N PHE A 162 " --> pdb=" O VAL A 158 " (cutoff:3.500A) Proline residue: A 163 - end of helix Processing helix chain 'A' and resid 172 through 193 removed outlier: 3.712A pdb=" N THR A 176 " --> pdb=" O GLY A 172 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N GLY A 193 " --> pdb=" O TRP A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 219 removed outlier: 3.555A pdb=" N THR A 203 " --> pdb=" O LEU A 199 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N VAL A 215 " --> pdb=" O SER A 211 " (cutoff:3.500A) removed outlier: 3.881A pdb=" N PHE A 216 " --> pdb=" O VAL A 212 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLY A 219 " --> pdb=" O VAL A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 229 removed outlier: 4.349A pdb=" N ARG A 223 " --> pdb=" O GLY A 219 " (cutoff:3.500A) Processing helix chain 'A' and resid 230 through 232 No H-bonds generated for 'chain 'A' and resid 230 through 232' Processing helix chain 'A' and resid 233 through 260 removed outlier: 3.502A pdb=" N THR A 249 " --> pdb=" O ASN A 245 " (cutoff:3.500A) Proline residue: A 256 - end of helix Processing helix chain 'A' and resid 266 through 296 Processing helix chain 'A' and resid 305 through 313 removed outlier: 3.777A pdb=" N ASP A 313 " --> pdb=" O ALA A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 319 removed outlier: 6.226A pdb=" N GLU A 317 " --> pdb=" O SER A 314 " (cutoff:3.500A) removed outlier: 4.342A pdb=" N GLU A 318 " --> pdb=" O PRO A 315 " (cutoff:3.500A) Processing helix chain 'A' and resid 320 through 329 removed outlier: 3.542A pdb=" N PHE A 329 " --> pdb=" O ILE A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 331 through 363 removed outlier: 3.709A pdb=" N VAL A 335 " --> pdb=" O ASN A 331 " (cutoff:3.500A) removed outlier: 5.076A pdb=" N ASN A 356 " --> pdb=" O SER A 352 " (cutoff:3.500A) removed outlier: 5.632A pdb=" N GLN A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N THR A 361 " --> pdb=" O GLN A 357 " (cutoff:3.500A) removed outlier: 4.050A pdb=" N TYR A 362 " --> pdb=" O MET A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 393 removed outlier: 4.112A pdb=" N GLY A 381 " --> pdb=" O LEU A 377 " (cutoff:3.500A) removed outlier: 4.666A pdb=" N ASP A 393 " --> pdb=" O GLY A 389 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 418 removed outlier: 3.518A pdb=" N MET A 413 " --> pdb=" O SER A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 419 through 423 Processing helix chain 'A' and resid 424 through 440 removed outlier: 3.721A pdb=" N VAL A 428 " --> pdb=" O TYR A 424 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N PHE A 438 " --> pdb=" O VAL A 434 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N THR A 440 " --> pdb=" O GLY A 436 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 453 Processing helix chain 'A' and resid 458 through 489 removed outlier: 3.768A pdb=" N SER A 462 " --> pdb=" O SER A 458 " (cutoff:3.500A) Processing helix chain 'A' and resid 489 through 511 removed outlier: 3.556A pdb=" N LEU A 497 " --> pdb=" O GLY A 493 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N ILE A 511 " --> pdb=" O LEU A 507 " (cutoff:3.500A) 255 hydrogen bonds defined for protein. 756 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: 0.91 Time building geometry restraints manager: 1.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 961 1.34 - 1.46: 641 1.46 - 1.57: 1693 1.57 - 1.69: 0 1.69 - 1.81: 28 Bond restraints: 3323 Sorted by residual: bond pdb=" N ILE A 427 " pdb=" CA ILE A 427 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.30e-02 5.92e+03 7.52e+00 bond pdb=" N GLN A 308 " pdb=" CA GLN A 308 " ideal model delta sigma weight residual 1.458 1.488 -0.030 1.30e-02 5.92e+03 5.28e+00 bond pdb=" N ASP A 169 " pdb=" CA ASP A 169 " ideal model delta sigma weight residual 1.457 1.486 -0.030 1.33e-02 5.65e+03 4.95e+00 bond pdb=" CB GLN A 306 " pdb=" CG GLN A 306 " ideal model delta sigma weight residual 1.520 1.550 -0.030 3.00e-02 1.11e+03 9.82e-01 bond pdb=" C ILE A 427 " pdb=" N VAL A 428 " ideal model delta sigma weight residual 1.335 1.324 0.011 1.20e-02 6.94e+03 8.92e-01 ... (remaining 3318 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.69: 4444 1.69 - 3.39: 66 3.39 - 5.08: 16 5.08 - 6.77: 7 6.77 - 8.47: 1 Bond angle restraints: 4534 Sorted by residual: angle pdb=" C ALA A 307 " pdb=" N GLN A 308 " pdb=" CA GLN A 308 " ideal model delta sigma weight residual 120.68 115.80 4.88 1.70e+00 3.46e-01 8.23e+00 angle pdb=" N GLN A 308 " pdb=" CA GLN A 308 " pdb=" C GLN A 308 " ideal model delta sigma weight residual 112.23 108.88 3.35 1.26e+00 6.30e-01 7.09e+00 angle pdb=" N LEU A 220 " pdb=" CA LEU A 220 " pdb=" C LEU A 220 " ideal model delta sigma weight residual 109.81 115.56 -5.75 2.21e+00 2.05e-01 6.76e+00 angle pdb=" N LYS A 396 " pdb=" CA LYS A 396 " pdb=" C LYS A 396 " ideal model delta sigma weight residual 108.34 111.55 -3.21 1.31e+00 5.83e-01 6.02e+00 angle pdb=" CA LEU A 269 " pdb=" CB LEU A 269 " pdb=" CG LEU A 269 " ideal model delta sigma weight residual 116.30 124.77 -8.47 3.50e+00 8.16e-02 5.85e+00 ... (remaining 4529 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.51: 1697 17.51 - 35.02: 168 35.02 - 52.53: 34 52.53 - 70.05: 13 70.05 - 87.56: 2 Dihedral angle restraints: 1914 sinusoidal: 714 harmonic: 1200 Sorted by residual: dihedral pdb=" CA ASP A 421 " pdb=" CB ASP A 421 " pdb=" CG ASP A 421 " pdb=" OD1 ASP A 421 " ideal model delta sinusoidal sigma weight residual -30.00 -86.73 56.73 1 2.00e+01 2.50e-03 1.08e+01 dihedral pdb=" CA TYR A 117 " pdb=" C TYR A 117 " pdb=" N SER A 118 " pdb=" CA SER A 118 " ideal model delta harmonic sigma weight residual 180.00 163.76 16.24 0 5.00e+00 4.00e-02 1.05e+01 dihedral pdb=" CA THR A 440 " pdb=" C THR A 440 " pdb=" N GLY A 441 " pdb=" CA GLY A 441 " ideal model delta harmonic sigma weight residual 180.00 164.17 15.83 0 5.00e+00 4.00e-02 1.00e+01 ... (remaining 1911 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 316 0.026 - 0.051: 130 0.051 - 0.077: 66 0.077 - 0.102: 23 0.102 - 0.128: 8 Chirality restraints: 543 Sorted by residual: chirality pdb=" CA ILE A 427 " pdb=" N ILE A 427 " pdb=" C ILE A 427 " pdb=" CB ILE A 427 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.07e-01 chirality pdb=" CA PRO A 221 " pdb=" N PRO A 221 " pdb=" C PRO A 221 " pdb=" CB PRO A 221 " both_signs ideal model delta sigma weight residual False 2.72 2.61 0.11 2.00e-01 2.50e+01 3.15e-01 chirality pdb=" CA TYR A 117 " pdb=" N TYR A 117 " pdb=" C TYR A 117 " pdb=" CB TYR A 117 " both_signs ideal model delta sigma weight residual False 2.51 2.40 0.11 2.00e-01 2.50e+01 3.02e-01 ... (remaining 540 not shown) Planarity restraints: 550 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU A 443 " -0.022 5.00e-02 4.00e+02 3.35e-02 1.80e+00 pdb=" N PRO A 444 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 444 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 444 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 255 " -0.020 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO A 256 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 256 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 256 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 256 " 0.018 5.00e-02 4.00e+02 2.64e-02 1.11e+00 pdb=" N PRO A 257 " -0.046 5.00e-02 4.00e+02 pdb=" CA PRO A 257 " 0.013 5.00e-02 4.00e+02 pdb=" CD PRO A 257 " 0.015 5.00e-02 4.00e+02 ... (remaining 547 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1003 2.82 - 3.34: 3277 3.34 - 3.86: 5409 3.86 - 4.38: 6478 4.38 - 4.90: 10937 Nonbonded interactions: 27104 Sorted by model distance: nonbonded pdb=" ND2 ASN A 262 " pdb=" OE1 GLU A 367 " model vdw 2.301 3.120 nonbonded pdb=" O ILE A 415 " pdb=" OG1 THR A 419 " model vdw 2.380 3.040 nonbonded pdb=" OH TYR A 319 " pdb=" OG SER A 458 " model vdw 2.383 3.040 nonbonded pdb=" O GLY A 504 " pdb=" OG1 THR A 508 " model vdw 2.419 3.040 nonbonded pdb=" NE1 TRP A 189 " pdb=" OG1 THR A 286 " model vdw 2.424 3.120 ... (remaining 27099 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 12.860 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3323 Z= 0.191 Angle : 0.571 8.467 4534 Z= 0.294 Chirality : 0.038 0.128 543 Planarity : 0.003 0.034 550 Dihedral : 15.225 87.558 1150 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 0.00 % Allowed : 20.11 % 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 (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: 0.62 (0.39), residues: 415 helix: 0.91 (0.28), residues: 324 sheet: None (None), residues: 0 loop : -1.18 (0.58), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.008 0.001 PHE A 162 TYR 0.016 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.336 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 40 average time/residue: 1.3933 time to fit residues: 57.3634 Evaluate side-chains 37 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 16 optimal weight: 0.0010 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 369 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3243 r_free = 0.3243 target = 0.107386 restraints weight = 4006.688| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.15 r_work: 0.3042 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2917 rms_B_bonded: 4.66 restraints_weight: 0.2500 r_work (final): 0.2917 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7555 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3323 Z= 0.199 Angle : 0.610 7.432 4534 Z= 0.312 Chirality : 0.040 0.152 543 Planarity : 0.004 0.031 550 Dihedral : 4.104 15.377 446 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 18.70 % Favored : 79.60 % 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: 1.61 (0.41), residues: 415 helix: 1.69 (0.28), residues: 335 sheet: None (None), residues: 0 loop : -1.61 (0.58), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 500 HIS 0.001 0.000 HIS A 198 PHE 0.010 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.001 0.000 ARG A 107 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 49 time to evaluate : 0.332 Fit side-chains REVERT: A 136 GLU cc_start: 0.6759 (mt-10) cc_final: 0.6475 (mt-10) REVERT: A 169 ASP cc_start: 0.7569 (m-30) cc_final: 0.7184 (m-30) REVERT: A 390 LEU cc_start: 0.7428 (mt) cc_final: 0.6649 (tt) REVERT: A 409 SER cc_start: 0.9003 (t) cc_final: 0.8752 (m) outliers start: 6 outliers final: 1 residues processed: 53 average time/residue: 1.1057 time to fit residues: 60.5749 Evaluate side-chains 43 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 42 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 1 optimal weight: 0.8980 chunk 30 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3568 r_free = 0.3568 target = 0.135551 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3240 r_free = 0.3240 target = 0.107192 restraints weight = 3984.530| |-----------------------------------------------------------------------------| r_work (start): 0.3196 rms_B_bonded: 2.19 r_work: 0.3080 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2957 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7597 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3323 Z= 0.206 Angle : 0.592 8.895 4534 Z= 0.299 Chirality : 0.040 0.149 543 Planarity : 0.004 0.030 550 Dihedral : 4.032 14.791 446 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.83 % Allowed : 18.98 % Favored : 78.19 % 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: 1.78 (0.41), residues: 415 helix: 1.90 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.88 (0.57), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.005 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 47 time to evaluate : 0.369 Fit side-chains REVERT: A 136 GLU cc_start: 0.6854 (OUTLIER) cc_final: 0.6477 (mt-10) REVERT: A 390 LEU cc_start: 0.7573 (mt) cc_final: 0.6808 (tt) REVERT: A 409 SER cc_start: 0.9042 (t) cc_final: 0.8812 (m) outliers start: 10 outliers final: 2 residues processed: 52 average time/residue: 1.0978 time to fit residues: 59.0982 Evaluate side-chains 45 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 42 time to evaluate : 0.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 413 MET Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 36 optimal weight: 0.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.9980 chunk 19 optimal weight: 0.9990 chunk 2 optimal weight: 0.6980 chunk 14 optimal weight: 0.6980 chunk 31 optimal weight: 0.6980 chunk 24 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3564 r_free = 0.3564 target = 0.135667 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.106936 restraints weight = 4113.709| |-----------------------------------------------------------------------------| r_work (start): 0.3185 rms_B_bonded: 2.20 r_work: 0.3076 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2961 rms_B_bonded: 4.65 restraints_weight: 0.2500 r_work (final): 0.2961 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7529 moved from start: 0.2028 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3323 Z= 0.193 Angle : 0.586 8.610 4534 Z= 0.294 Chirality : 0.040 0.153 543 Planarity : 0.004 0.030 550 Dihedral : 4.041 15.242 446 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 3.40 % Allowed : 19.26 % Favored : 77.34 % 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: 1.93 (0.42), residues: 415 helix: 2.02 (0.29), residues: 332 sheet: None (None), residues: 0 loop : -1.88 (0.57), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.005 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 44 time to evaluate : 0.385 Fit side-chains REVERT: A 126 ILE cc_start: 0.8862 (tp) cc_final: 0.8553 (tp) REVERT: A 136 GLU cc_start: 0.6788 (OUTLIER) cc_final: 0.6312 (mt-10) REVERT: A 388 CYS cc_start: 0.6687 (OUTLIER) cc_final: 0.5517 (m) REVERT: A 390 LEU cc_start: 0.7450 (mt) cc_final: 0.6634 (tt) REVERT: A 409 SER cc_start: 0.8964 (t) cc_final: 0.8726 (m) outliers start: 12 outliers final: 2 residues processed: 51 average time/residue: 1.1491 time to fit residues: 60.7791 Evaluate side-chains 45 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 41 time to evaluate : 0.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 30 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 0 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 9 optimal weight: 3.9990 chunk 3 optimal weight: 0.9990 chunk 11 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3531 r_free = 0.3531 target = 0.133040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104211 restraints weight = 4116.399| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.20 r_work: 0.3032 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2914 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7752 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3323 Z= 0.199 Angle : 0.574 7.724 4534 Z= 0.290 Chirality : 0.039 0.154 543 Planarity : 0.004 0.030 550 Dihedral : 4.035 15.812 446 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 4.25 % Allowed : 18.98 % Favored : 76.77 % 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: 2.09 (0.41), residues: 415 helix: 2.17 (0.29), residues: 326 sheet: None (None), residues: 0 loop : -1.71 (0.56), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.009 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.006 0.000 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 43 time to evaluate : 0.339 Fit side-chains REVERT: A 126 ILE cc_start: 0.9023 (tp) cc_final: 0.8706 (tp) REVERT: A 136 GLU cc_start: 0.7077 (OUTLIER) cc_final: 0.6601 (mt-10) REVERT: A 154 MET cc_start: 0.9158 (OUTLIER) cc_final: 0.8870 (mtm) REVERT: A 388 CYS cc_start: 0.6654 (OUTLIER) cc_final: 0.5518 (m) REVERT: A 390 LEU cc_start: 0.7501 (OUTLIER) cc_final: 0.6699 (tt) REVERT: A 409 SER cc_start: 0.9061 (t) cc_final: 0.8776 (m) outliers start: 15 outliers final: 1 residues processed: 50 average time/residue: 1.1334 time to fit residues: 58.5859 Evaluate side-chains 46 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 154 MET Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 440 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 18 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 0.0980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 35 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 37 optimal weight: 0.6980 chunk 22 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3563 r_free = 0.3563 target = 0.135913 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.107508 restraints weight = 4187.209| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.17 r_work: 0.3047 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7553 moved from start: 0.2263 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3323 Z= 0.172 Angle : 0.561 7.498 4534 Z= 0.282 Chirality : 0.039 0.150 543 Planarity : 0.004 0.030 550 Dihedral : 3.978 16.343 446 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 2.27 % Allowed : 21.81 % Favored : 75.92 % 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: 2.17 (0.41), residues: 415 helix: 2.21 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.72 (0.57), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.006 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.335 Fit side-chains REVERT: A 126 ILE cc_start: 0.8833 (tp) cc_final: 0.8546 (tp) REVERT: A 128 TYR cc_start: 0.8468 (m-80) cc_final: 0.7850 (m-80) REVERT: A 136 GLU cc_start: 0.6815 (OUTLIER) cc_final: 0.6358 (mt-10) REVERT: A 388 CYS cc_start: 0.6277 (OUTLIER) cc_final: 0.5462 (m) REVERT: A 390 LEU cc_start: 0.7458 (mt) cc_final: 0.6714 (tt) REVERT: A 409 SER cc_start: 0.8957 (t) cc_final: 0.8718 (m) REVERT: A 445 LEU cc_start: 0.8289 (OUTLIER) cc_final: 0.7937 (mm) outliers start: 8 outliers final: 1 residues processed: 55 average time/residue: 1.1585 time to fit residues: 65.7468 Evaluate side-chains 43 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 39 time to evaluate : 0.348 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 5 optimal weight: 0.5980 chunk 25 optimal weight: 0.7980 chunk 2 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3555 r_free = 0.3555 target = 0.134980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3217 r_free = 0.3217 target = 0.106541 restraints weight = 4148.090| |-----------------------------------------------------------------------------| r_work (start): 0.3112 rms_B_bonded: 2.17 r_work: 0.3000 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.2886 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2886 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3323 Z= 0.192 Angle : 0.570 7.830 4534 Z= 0.287 Chirality : 0.039 0.153 543 Planarity : 0.004 0.030 550 Dihedral : 4.013 16.570 446 Min Nonbonded Distance : 2.588 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.12 % Allowed : 22.10 % Favored : 74.79 % 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: 2.22 (0.42), residues: 415 helix: 2.25 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.72 (0.55), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.007 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.325 Fit side-chains REVERT: A 126 ILE cc_start: 0.8808 (tp) cc_final: 0.8522 (tp) REVERT: A 136 GLU cc_start: 0.6787 (OUTLIER) cc_final: 0.6299 (mt-10) REVERT: A 279 TYR cc_start: 0.6759 (t80) cc_final: 0.5604 (m-80) REVERT: A 388 CYS cc_start: 0.6389 (OUTLIER) cc_final: 0.5638 (m) REVERT: A 390 LEU cc_start: 0.7364 (OUTLIER) cc_final: 0.6599 (tt) REVERT: A 409 SER cc_start: 0.8951 (t) cc_final: 0.8692 (m) REVERT: A 445 LEU cc_start: 0.8264 (OUTLIER) cc_final: 0.7914 (mm) REVERT: A 512 LYS cc_start: 0.7906 (ptmm) cc_final: 0.7699 (pttt) outliers start: 11 outliers final: 3 residues processed: 48 average time/residue: 1.1406 time to fit residues: 56.5808 Evaluate side-chains 45 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 15 optimal weight: 0.3980 chunk 4 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 17 optimal weight: 0.6980 chunk 28 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3560 r_free = 0.3560 target = 0.135600 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.107161 restraints weight = 4156.415| |-----------------------------------------------------------------------------| r_work (start): 0.3120 rms_B_bonded: 2.16 r_work: 0.3009 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2896 rms_B_bonded: 4.60 restraints_weight: 0.2500 r_work (final): 0.2896 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7500 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3323 Z= 0.181 Angle : 0.567 7.323 4534 Z= 0.286 Chirality : 0.039 0.153 543 Planarity : 0.004 0.030 550 Dihedral : 3.989 15.744 446 Min Nonbonded Distance : 2.566 Molprobity Statistics. All-atom Clashscore : 6.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 3.12 % Allowed : 22.66 % Favored : 74.22 % 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: 2.32 (0.42), residues: 415 helix: 2.33 (0.29), residues: 328 sheet: None (None), residues: 0 loop : -1.72 (0.56), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.007 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 41 time to evaluate : 0.348 Fit side-chains REVERT: A 126 ILE cc_start: 0.8779 (tp) cc_final: 0.8505 (tp) REVERT: A 136 GLU cc_start: 0.6768 (OUTLIER) cc_final: 0.6283 (mt-10) REVERT: A 154 MET cc_start: 0.9024 (mtm) cc_final: 0.8746 (mtm) REVERT: A 279 TYR cc_start: 0.6729 (t80) cc_final: 0.5570 (m-80) REVERT: A 388 CYS cc_start: 0.6227 (OUTLIER) cc_final: 0.5499 (m) REVERT: A 390 LEU cc_start: 0.7360 (OUTLIER) cc_final: 0.6602 (tt) REVERT: A 409 SER cc_start: 0.8933 (t) cc_final: 0.8687 (m) REVERT: A 445 LEU cc_start: 0.8280 (OUTLIER) cc_final: 0.7910 (mm) outliers start: 11 outliers final: 2 residues processed: 50 average time/residue: 1.1356 time to fit residues: 58.6747 Evaluate side-chains 45 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 39 time to evaluate : 0.380 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 390 LEU Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 8 optimal weight: 3.9990 chunk 16 optimal weight: 0.0470 chunk 4 optimal weight: 0.5980 chunk 35 optimal weight: 3.9990 chunk 20 optimal weight: 0.0670 chunk 40 optimal weight: 0.5980 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 3.9990 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3587 r_free = 0.3587 target = 0.138279 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.110209 restraints weight = 4198.335| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.16 r_work: 0.3126 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3013 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3013 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7546 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3323 Z= 0.161 Angle : 0.561 8.630 4534 Z= 0.281 Chirality : 0.038 0.150 543 Planarity : 0.004 0.031 550 Dihedral : 3.924 15.686 446 Min Nonbonded Distance : 2.554 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 1.98 % Allowed : 23.80 % Favored : 74.22 % 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: 2.44 (0.42), residues: 415 helix: 2.37 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.52 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 500 HIS 0.000 0.000 HIS A 145 PHE 0.011 0.001 PHE A 496 TYR 0.024 0.001 TYR A 117 ARG 0.008 0.001 ARG A 174 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 42 time to evaluate : 0.334 Fit side-chains REVERT: A 126 ILE cc_start: 0.8807 (tp) cc_final: 0.8539 (tp) REVERT: A 136 GLU cc_start: 0.6775 (OUTLIER) cc_final: 0.6323 (mt-10) REVERT: A 154 MET cc_start: 0.9073 (mtm) cc_final: 0.8802 (mtm) REVERT: A 279 TYR cc_start: 0.6783 (t80) cc_final: 0.5606 (m-80) REVERT: A 388 CYS cc_start: 0.6366 (OUTLIER) cc_final: 0.5723 (m) REVERT: A 445 LEU cc_start: 0.8306 (OUTLIER) cc_final: 0.7950 (mm) REVERT: A 512 LYS cc_start: 0.7552 (pttp) cc_final: 0.7342 (pttp) outliers start: 7 outliers final: 3 residues processed: 49 average time/residue: 1.1605 time to fit residues: 58.7040 Evaluate side-chains 42 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 36 time to evaluate : 0.317 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 275 SER Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 19 optimal weight: 4.9990 chunk 12 optimal weight: 0.9980 chunk 24 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 1 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 38 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3558 r_free = 0.3558 target = 0.135332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.106921 restraints weight = 4104.644| |-----------------------------------------------------------------------------| r_work (start): 0.3161 rms_B_bonded: 2.16 r_work: 0.3051 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2937 rms_B_bonded: 4.62 restraints_weight: 0.2500 r_work (final): 0.2937 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7573 moved from start: 0.2486 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3323 Z= 0.194 Angle : 0.581 8.759 4534 Z= 0.292 Chirality : 0.039 0.155 543 Planarity : 0.004 0.035 550 Dihedral : 4.001 15.906 446 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.98 % Allowed : 24.65 % Favored : 73.37 % 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: 2.38 (0.42), residues: 415 helix: 2.33 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.54 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 500 HIS 0.001 0.000 HIS A 145 PHE 0.010 0.001 PHE A 496 TYR 0.025 0.001 TYR A 117 ARG 0.007 0.001 ARG A 174 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 830 Ramachandran restraints generated. 415 Oldfield, 0 Emsley, 415 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 38 time to evaluate : 0.344 Fit side-chains REVERT: A 126 ILE cc_start: 0.8831 (tp) cc_final: 0.8553 (tp) REVERT: A 136 GLU cc_start: 0.6861 (OUTLIER) cc_final: 0.6383 (mt-10) REVERT: A 154 MET cc_start: 0.9117 (mtm) cc_final: 0.8812 (mtm) REVERT: A 279 TYR cc_start: 0.6824 (t80) cc_final: 0.5662 (m-80) REVERT: A 388 CYS cc_start: 0.6260 (OUTLIER) cc_final: 0.5618 (m) REVERT: A 445 LEU cc_start: 0.8325 (OUTLIER) cc_final: 0.7937 (mm) outliers start: 7 outliers final: 2 residues processed: 45 average time/residue: 1.1364 time to fit residues: 52.9120 Evaluate side-chains 42 residues out of total 353 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 37 time to evaluate : 0.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 136 GLU Chi-restraints excluded: chain A residue 299 LYS Chi-restraints excluded: chain A residue 388 CYS Chi-restraints excluded: chain A residue 440 THR Chi-restraints excluded: chain A residue 445 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 14 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 39 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 2 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3534 r_free = 0.3534 target = 0.133188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.104299 restraints weight = 4164.774| |-----------------------------------------------------------------------------| r_work (start): 0.3188 rms_B_bonded: 2.20 r_work: 0.3080 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.2966 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.2966 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3323 Z= 0.201 Angle : 0.585 8.655 4534 Z= 0.294 Chirality : 0.039 0.156 543 Planarity : 0.004 0.033 550 Dihedral : 4.018 15.769 446 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.70 % Allowed : 24.08 % Favored : 74.22 % 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: 2.39 (0.42), residues: 415 helix: 2.33 (0.29), residues: 329 sheet: None (None), residues: 0 loop : -1.49 (0.57), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 500 HIS 0.001 0.001 HIS A 145 PHE 0.010 0.001 PHE A 162 TYR 0.025 0.001 TYR A 117 ARG 0.007 0.001 ARG A 174 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2287.11 seconds wall clock time: 41 minutes 24.08 seconds (2484.08 seconds total)