Starting phenix.real_space_refine on Thu Jul 24 16:14:59 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9cfg_45545/07_2025/9cfg_45545.cif Found real_map, /net/cci-nas-00/data/ceres_data/9cfg_45545/07_2025/9cfg_45545.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/9cfg_45545/07_2025/9cfg_45545.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9cfg_45545/07_2025/9cfg_45545.map" model { file = "/net/cci-nas-00/data/ceres_data/9cfg_45545/07_2025/9cfg_45545.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9cfg_45545/07_2025/9cfg_45545.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= -0.000 sd= 0.009 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians S 14 5.16 5 C 2076 2.51 5 N 551 2.21 5 O 619 1.98 5 H 3140 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 16 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/modules/chem_data/mon_lib" Total number of atoms: 6400 Number of models: 1 Model: "" Number of chains: 3 Chain: "H" Number of atoms: 1740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 115, 1740 Classifications: {'peptide': 115} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PTRANS': 4, 'TRANS': 110} Chain: "L" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 1653 Classifications: {'peptide': 108} Modifications used: {'COO': 1, 'NH3': 1} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 100} Chain: "A" Number of atoms: 3007 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 3007 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 14, 'TRANS': 179} Time building chain proxies: 4.62, per 1000 atoms: 0.72 Number of scatterers: 6400 At special positions: 0 Unit cell: (67.23, 85.49, 89.64, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 O 619 8.00 N 551 7.00 C 2076 6.00 H 3140 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 95 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 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: 1.59 Conformation dependent library (CDL) restraints added in 612.8 milliseconds 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 762 Finding SS restraints... Secondary structure from input PDB file: 8 helices and 9 sheets defined 11.5% alpha, 30.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'H' and resid 28 through 32 Processing helix chain 'H' and resid 86 through 90 Processing helix chain 'A' and resid 337 through 343 Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.412A pdb=" N ILE A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 389 removed outlier: 3.557A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.705A pdb=" N MET H 34 " --> pdb=" O VAL H 50 " (cutoff:3.500A) removed outlier: 4.405A pdb=" N VAL H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.600A pdb=" N TRP H 36 " --> pdb=" O LEU H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 11 through 12 Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.607A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.554A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 354 through 358 removed outlier: 3.546A pdb=" N ASN A 354 " --> pdb=" O SER A 399 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 391 through 392 Processing sheet with id=AA8, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA9, first strand: chain 'A' and resid 473 through 474 114 hydrogen bonds defined for protein. 264 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: 2.52 Time building geometry restraints manager: 1.94 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 3140 1.03 - 1.23: 5 1.23 - 1.42: 1470 1.42 - 1.62: 1856 1.62 - 1.82: 16 Bond restraints: 6487 Sorted by residual: bond pdb=" N GLU H 1 " pdb=" H3 GLU H 1 " ideal model delta sigma weight residual 0.890 0.961 -0.071 2.00e-02 2.50e+03 1.24e+01 bond pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N GLU L 1 " pdb=" H2 GLU L 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.23e+01 bond pdb=" N GLU H 1 " pdb=" H2 GLU H 1 " ideal model delta sigma weight residual 0.890 0.960 -0.070 2.00e-02 2.50e+03 1.22e+01 bond pdb=" N ASN A 334 " pdb=" CA ASN A 334 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.90e-02 2.77e+03 2.91e+00 ... (remaining 6482 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.20: 11630 4.20 - 8.41: 25 8.41 - 12.61: 1 12.61 - 16.81: 1 16.81 - 21.01: 2 Bond angle restraints: 11659 Sorted by residual: angle pdb=" H1 GLU L 1 " pdb=" N GLU L 1 " pdb=" H2 GLU L 1 " ideal model delta sigma weight residual 109.47 88.46 21.01 3.00e+00 1.11e-01 4.91e+01 angle pdb=" H1 GLU H 1 " pdb=" N GLU H 1 " pdb=" H3 GLU H 1 " ideal model delta sigma weight residual 109.47 92.08 17.39 3.00e+00 1.11e-01 3.36e+01 angle pdb=" H1 GLU L 1 " pdb=" N GLU L 1 " pdb=" H3 GLU L 1 " ideal model delta sigma weight residual 109.47 123.45 -13.98 3.00e+00 1.11e-01 2.17e+01 angle pdb=" H1 GLU H 1 " pdb=" N GLU H 1 " pdb=" H2 GLU H 1 " ideal model delta sigma weight residual 109.47 120.66 -11.19 3.00e+00 1.11e-01 1.39e+01 angle pdb=" CG LYS A 386 " pdb=" CD LYS A 386 " pdb=" CE LYS A 386 " ideal model delta sigma weight residual 111.30 119.71 -8.41 2.30e+00 1.89e-01 1.34e+01 ... (remaining 11654 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 2774 17.98 - 35.96: 255 35.96 - 53.95: 73 53.95 - 71.93: 22 71.93 - 89.91: 4 Dihedral angle restraints: 3128 sinusoidal: 1663 harmonic: 1465 Sorted by residual: dihedral pdb=" CA LYS A 478 " pdb=" C LYS A 478 " pdb=" N PRO A 479 " pdb=" CA PRO A 479 " ideal model delta harmonic sigma weight residual 180.00 160.43 19.57 0 5.00e+00 4.00e-02 1.53e+01 dihedral pdb=" CA LEU A 518 " pdb=" C LEU A 518 " pdb=" N HIS A 519 " pdb=" CA HIS A 519 " ideal model delta harmonic sigma weight residual 180.00 160.83 19.17 0 5.00e+00 4.00e-02 1.47e+01 dihedral pdb=" CA PRO A 373 " pdb=" C PRO A 373 " pdb=" N PHE A 374 " pdb=" CA PHE A 374 " ideal model delta harmonic sigma weight residual 180.00 163.49 16.51 0 5.00e+00 4.00e-02 1.09e+01 ... (remaining 3125 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 260 0.028 - 0.056: 147 0.056 - 0.083: 38 0.083 - 0.111: 29 0.111 - 0.139: 13 Chirality restraints: 487 Sorted by residual: chirality pdb=" CA VAL L 58 " pdb=" N VAL L 58 " pdb=" C VAL L 58 " pdb=" CB VAL L 58 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.81e-01 chirality pdb=" CA ILE L 75 " pdb=" N ILE L 75 " pdb=" C ILE L 75 " pdb=" CB ILE L 75 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.24e-01 ... (remaining 484 not shown) Planarity restraints: 983 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 372 " 0.036 5.00e-02 4.00e+02 5.29e-02 4.48e+00 pdb=" N PRO A 373 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 373 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 373 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE L 14 " 0.028 5.00e-02 4.00e+02 4.22e-02 2.85e+00 pdb=" N PRO L 15 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO L 15 " 0.022 5.00e-02 4.00e+02 pdb=" CD PRO L 15 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 338 " -0.009 2.00e-02 2.50e+03 8.41e-03 2.12e+00 pdb=" CG PHE A 338 " 0.025 2.00e-02 2.50e+03 pdb=" CD1 PHE A 338 " -0.010 2.00e-02 2.50e+03 pdb=" CD2 PHE A 338 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 PHE A 338 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE A 338 " 0.002 2.00e-02 2.50e+03 pdb=" CZ PHE A 338 " 0.000 2.00e-02 2.50e+03 pdb=" HD1 PHE A 338 " 0.002 2.00e-02 2.50e+03 pdb=" HD2 PHE A 338 " 0.000 2.00e-02 2.50e+03 pdb=" HE1 PHE A 338 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 338 " -0.002 2.00e-02 2.50e+03 pdb=" HZ PHE A 338 " 0.000 2.00e-02 2.50e+03 ... (remaining 980 not shown) Histogram of nonbonded interaction distances: 1.60 - 2.20: 446 2.20 - 2.80: 12987 2.80 - 3.40: 18135 3.40 - 4.00: 24751 4.00 - 4.60: 36700 Nonbonded interactions: 93019 Sorted by model distance: nonbonded pdb=" OE1 GLU L 81 " pdb=" H GLU L 81 " model vdw 1.597 2.450 nonbonded pdb="HD22 ASN A 422 " pdb=" O ARG A 454 " model vdw 1.622 2.450 nonbonded pdb=" H ASN A 405 " pdb=" O GLY A 504 " model vdw 1.651 2.450 nonbonded pdb=" OD1 ASN A 422 " pdb=" H ARG A 454 " model vdw 1.673 2.450 nonbonded pdb=" OE1 GLN H 39 " pdb="HE21 GLN L 38 " model vdw 1.685 2.450 ... (remaining 93014 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.920 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: 0.110 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 19.770 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:17.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3353 Z= 0.167 Angle : 0.746 8.405 4566 Z= 0.387 Chirality : 0.044 0.139 487 Planarity : 0.005 0.053 594 Dihedral : 14.302 80.199 1200 Min Nonbonded Distance : 2.015 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 0.28 % Allowed : 20.85 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.59 (0.42), residues: 411 helix: -2.21 (0.88), residues: 29 sheet: -0.29 (0.49), residues: 121 loop : -0.13 (0.40), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 353 HIS 0.003 0.001 HIS A 339 PHE 0.025 0.001 PHE A 338 TYR 0.009 0.001 TYR L 49 ARG 0.007 0.001 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.23736 ( 109) hydrogen bonds : angle 10.09393 ( 264) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.80149 ( 12) covalent geometry : bond 0.00383 ( 3347) covalent geometry : angle 0.74573 ( 4554) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.558 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8923 (mtpp) cc_final: 0.8667 (mmmt) outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 1.8400 time to fit residues: 69.6559 Evaluate side-chains 35 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 34 time to evaluate : 0.519 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 50 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 36 optimal weight: 0.4980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 343 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4048 r_free = 0.4048 target = 0.082954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.067746 restraints weight = 34322.508| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 4.76 r_work: 0.3576 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3576 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7678 moved from start: 0.1247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3353 Z= 0.126 Angle : 0.577 4.407 4566 Z= 0.294 Chirality : 0.044 0.134 487 Planarity : 0.005 0.037 594 Dihedral : 4.924 24.228 464 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.14 % Favored : 95.62 % Rotamer: Outliers : 3.38 % Allowed : 17.18 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.73 (0.41), residues: 411 helix: -2.31 (0.81), residues: 29 sheet: -0.45 (0.48), residues: 113 loop : -0.21 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 505 PHE 0.014 0.001 PHE A 338 TYR 0.012 0.001 TYR L 49 ARG 0.002 0.000 ARG L 24 Details of bonding type rmsd hydrogen bonds : bond 0.03828 ( 109) hydrogen bonds : angle 6.58314 ( 264) SS BOND : bond 0.00329 ( 6) SS BOND : angle 0.61269 ( 12) covalent geometry : bond 0.00287 ( 3347) covalent geometry : angle 0.57661 ( 4554) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 49 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 37 time to evaluate : 0.594 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8939 (mtpp) cc_final: 0.8651 (mmmt) outliers start: 12 outliers final: 5 residues processed: 45 average time/residue: 2.1464 time to fit residues: 100.7611 Evaluate side-chains 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 36 time to evaluate : 0.528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain L residue 50 ASP Chi-restraints excluded: chain A residue 339 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 35 optimal weight: 5.9990 chunk 12 optimal weight: 0.0070 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 22 optimal weight: 3.9990 chunk 27 optimal weight: 0.5980 chunk 32 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 8 optimal weight: 5.9990 overall best weight: 0.6600 ------------------------------------------------------------------------------- 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 = 0.4048 r_free = 0.4048 target = 0.082474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.066973 restraints weight = 34566.309| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 4.90 r_work: 0.3560 rms_B_bonded: 4.99 restraints_weight: 0.5000 r_work (final): 0.3560 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7679 moved from start: 0.1660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3353 Z= 0.118 Angle : 0.558 4.887 4566 Z= 0.279 Chirality : 0.043 0.134 487 Planarity : 0.004 0.038 594 Dihedral : 4.709 22.263 464 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 3.38 % Allowed : 16.90 % Favored : 79.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.43 (0.42), residues: 411 helix: -2.13 (0.88), residues: 29 sheet: -0.17 (0.45), residues: 130 loop : -0.00 (0.41), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS L 31 PHE 0.007 0.001 PHE A 375 TYR 0.012 0.001 TYR A 369 ARG 0.004 0.001 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.03204 ( 109) hydrogen bonds : angle 5.97873 ( 264) SS BOND : bond 0.00285 ( 6) SS BOND : angle 0.63856 ( 12) covalent geometry : bond 0.00270 ( 3347) covalent geometry : angle 0.55750 ( 4554) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 36 time to evaluate : 1.914 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8942 (mtpp) cc_final: 0.8643 (mmmt) outliers start: 12 outliers final: 9 residues processed: 44 average time/residue: 2.4457 time to fit residues: 115.3097 Evaluate side-chains 42 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 33 time to evaluate : 2.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 77 THR Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 339 HIS Chi-restraints excluded: chain A residue 410 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 10 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 16 optimal weight: 0.4980 chunk 4 optimal weight: 2.9990 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.081277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3703 r_free = 0.3703 target = 0.066129 restraints weight = 35492.411| |-----------------------------------------------------------------------------| r_work (start): 0.3670 rms_B_bonded: 4.75 r_work: 0.3540 rms_B_bonded: 4.84 restraints_weight: 0.5000 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7687 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3353 Z= 0.143 Angle : 0.544 4.252 4566 Z= 0.274 Chirality : 0.042 0.132 487 Planarity : 0.004 0.041 594 Dihedral : 4.578 17.632 462 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.62 % Favored : 95.13 % Rotamer: Outliers : 2.25 % Allowed : 18.87 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.43 (0.42), residues: 411 helix: -2.28 (0.81), residues: 29 sheet: -0.13 (0.46), residues: 129 loop : -0.00 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.001 0.001 HIS A 519 PHE 0.006 0.001 PHE A 375 TYR 0.013 0.001 TYR A 369 ARG 0.003 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.02929 ( 109) hydrogen bonds : angle 5.75298 ( 264) SS BOND : bond 0.00259 ( 6) SS BOND : angle 0.60666 ( 12) covalent geometry : bond 0.00319 ( 3347) covalent geometry : angle 0.54352 ( 4554) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 34 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 386 LYS cc_start: 0.8946 (mtpp) cc_final: 0.8671 (mmmt) outliers start: 8 outliers final: 6 residues processed: 38 average time/residue: 2.8735 time to fit residues: 117.2250 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 1.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain A residue 336 CYS Chi-restraints excluded: chain A residue 440 LYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 1.9990 chunk 13 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 20 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 18 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 overall best weight: 0.9384 ------------------------------------------------------------------------------- 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 = 0.4016 r_free = 0.4016 target = 0.081040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3699 r_free = 0.3699 target = 0.066092 restraints weight = 35186.639| |-----------------------------------------------------------------------------| r_work (start): 0.3666 rms_B_bonded: 4.69 r_work: 0.3536 rms_B_bonded: 4.82 restraints_weight: 0.5000 r_work (final): 0.3536 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2168 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3353 Z= 0.136 Angle : 0.533 4.232 4566 Z= 0.268 Chirality : 0.042 0.133 487 Planarity : 0.004 0.041 594 Dihedral : 4.525 17.612 462 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.62 % Favored : 95.13 % Rotamer: Outliers : 1.97 % Allowed : 18.87 % Favored : 79.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.38 (0.42), residues: 411 helix: -2.18 (0.82), residues: 29 sheet: -0.07 (0.46), residues: 129 loop : -0.00 (0.41), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.001 0.001 HIS A 339 PHE 0.005 0.001 PHE A 375 TYR 0.013 0.001 TYR A 369 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02804 ( 109) hydrogen bonds : angle 5.66628 ( 264) SS BOND : bond 0.00230 ( 6) SS BOND : angle 0.53646 ( 12) covalent geometry : bond 0.00304 ( 3347) covalent geometry : angle 0.53283 ( 4554) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 32 time to evaluate : 0.524 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9223 (mp) cc_final: 0.8879 (tt) REVERT: A 386 LYS cc_start: 0.8940 (mtpp) cc_final: 0.8667 (mmmt) outliers start: 7 outliers final: 6 residues processed: 36 average time/residue: 1.7407 time to fit residues: 65.6551 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 30 time to evaluate : 0.522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 18 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 36 optimal weight: 0.7980 chunk 5 optimal weight: 0.4980 chunk 35 optimal weight: 0.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- 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 = 0.3990 r_free = 0.3990 target = 0.079863 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.064646 restraints weight = 35055.768| |-----------------------------------------------------------------------------| r_work (start): 0.3637 rms_B_bonded: 4.77 r_work: 0.3506 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.2399 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3353 Z= 0.171 Angle : 0.546 4.412 4566 Z= 0.276 Chirality : 0.042 0.134 487 Planarity : 0.004 0.042 594 Dihedral : 4.624 18.856 462 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 5.94 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.87 % Favored : 94.89 % Rotamer: Outliers : 2.82 % Allowed : 18.59 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.47 (0.42), residues: 411 helix: -2.08 (0.85), residues: 29 sheet: -0.15 (0.45), residues: 138 loop : -0.06 (0.41), residues: 244 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 PHE 0.006 0.001 PHE A 497 TYR 0.015 0.001 TYR A 369 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.02907 ( 109) hydrogen bonds : angle 5.62095 ( 264) SS BOND : bond 0.00237 ( 6) SS BOND : angle 0.58483 ( 12) covalent geometry : bond 0.00371 ( 3347) covalent geometry : angle 0.54555 ( 4554) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 33 time to evaluate : 0.473 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9230 (mp) cc_final: 0.8840 (tt) REVERT: A 386 LYS cc_start: 0.8943 (mtpp) cc_final: 0.8679 (mmmt) outliers start: 10 outliers final: 7 residues processed: 39 average time/residue: 1.5821 time to fit residues: 64.7645 Evaluate side-chains 38 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 31 time to evaluate : 0.505 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 38 optimal weight: 0.7980 chunk 14 optimal weight: 3.9990 chunk 3 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 26 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 22 optimal weight: 0.4980 chunk 28 optimal weight: 0.9980 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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 = 0.4018 r_free = 0.4018 target = 0.081310 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.066491 restraints weight = 35365.005| |-----------------------------------------------------------------------------| r_work (start): 0.3672 rms_B_bonded: 4.68 r_work: 0.3542 rms_B_bonded: 4.80 restraints_weight: 0.5000 r_work (final): 0.3542 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7729 moved from start: 0.2446 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3353 Z= 0.118 Angle : 0.522 4.595 4566 Z= 0.262 Chirality : 0.042 0.134 487 Planarity : 0.004 0.044 594 Dihedral : 4.428 17.040 462 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 1.69 % Allowed : 19.44 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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 (0.42), residues: 411 helix: -1.93 (0.85), residues: 29 sheet: -0.03 (0.46), residues: 129 loop : -0.04 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 PHE 0.005 0.001 PHE A 392 TYR 0.013 0.001 TYR A 369 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02619 ( 109) hydrogen bonds : angle 5.39662 ( 264) SS BOND : bond 0.00209 ( 6) SS BOND : angle 0.49815 ( 12) covalent geometry : bond 0.00266 ( 3347) covalent geometry : angle 0.52217 ( 4554) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 33 time to evaluate : 0.546 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9166 (mp) cc_final: 0.8812 (tt) REVERT: A 386 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8692 (mmmt) outliers start: 6 outliers final: 6 residues processed: 36 average time/residue: 1.7193 time to fit residues: 64.9381 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.561 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 82 MET Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 0 optimal weight: 4.9990 chunk 27 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 11 optimal weight: 4.9990 chunk 18 optimal weight: 6.9990 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 31 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.080340 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3683 r_free = 0.3683 target = 0.065317 restraints weight = 35047.406| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 4.78 r_work: 0.3525 rms_B_bonded: 4.88 restraints_weight: 0.5000 r_work (final): 0.3525 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.2558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3353 Z= 0.137 Angle : 0.528 4.985 4566 Z= 0.265 Chirality : 0.042 0.133 487 Planarity : 0.004 0.043 594 Dihedral : 4.417 17.179 462 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.84 % Favored : 93.92 % Rotamer: Outliers : 2.25 % Allowed : 18.87 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.34 (0.42), residues: 411 helix: -1.97 (0.85), residues: 29 sheet: -0.02 (0.46), residues: 129 loop : -0.02 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 PHE 0.005 0.001 PHE A 392 TYR 0.014 0.001 TYR A 369 ARG 0.002 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02667 ( 109) hydrogen bonds : angle 5.47691 ( 264) SS BOND : bond 0.00220 ( 6) SS BOND : angle 0.49859 ( 12) covalent geometry : bond 0.00303 ( 3347) covalent geometry : angle 0.52807 ( 4554) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 33 time to evaluate : 0.561 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9217 (mp) cc_final: 0.8806 (tt) REVERT: A 386 LYS cc_start: 0.8968 (mtpp) cc_final: 0.8698 (mmmt) outliers start: 8 outliers final: 6 residues processed: 38 average time/residue: 1.8544 time to fit residues: 73.5312 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 31 time to evaluate : 0.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 15 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.2980 chunk 16 optimal weight: 0.8980 chunk 36 optimal weight: 0.9990 chunk 6 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 39 optimal weight: 0.2980 chunk 4 optimal weight: 0.0270 overall best weight: 0.4638 ------------------------------------------------------------------------------- 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 = 0.4040 r_free = 0.4040 target = 0.081963 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.067020 restraints weight = 35438.348| |-----------------------------------------------------------------------------| r_work (start): 0.3694 rms_B_bonded: 4.80 r_work: 0.3562 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3562 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7704 moved from start: 0.2660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3353 Z= 0.103 Angle : 0.521 5.209 4566 Z= 0.260 Chirality : 0.043 0.133 487 Planarity : 0.004 0.044 594 Dihedral : 4.246 16.094 462 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 5.63 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.38 % Favored : 95.38 % Rotamer: Outliers : 1.69 % Allowed : 19.72 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.25 (0.42), residues: 411 helix: -1.92 (0.88), residues: 29 sheet: 0.15 (0.47), residues: 129 loop : -0.02 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 PHE 0.007 0.001 PHE A 392 TYR 0.014 0.001 TYR A 369 ARG 0.002 0.000 ARG L 61 Details of bonding type rmsd hydrogen bonds : bond 0.02501 ( 109) hydrogen bonds : angle 5.27736 ( 264) SS BOND : bond 0.00195 ( 6) SS BOND : angle 0.44776 ( 12) covalent geometry : bond 0.00242 ( 3347) covalent geometry : angle 0.52080 ( 4554) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.541 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9140 (mp) cc_final: 0.8749 (tt) REVERT: A 386 LYS cc_start: 0.8962 (mtpp) cc_final: 0.8687 (mmmt) outliers start: 6 outliers final: 5 residues processed: 38 average time/residue: 1.5653 time to fit residues: 62.7716 Evaluate side-chains 37 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 32 time to evaluate : 0.631 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 4.9990 chunk 33 optimal weight: 0.2980 chunk 20 optimal weight: 0.7980 chunk 10 optimal weight: 0.2980 chunk 1 optimal weight: 1.9990 chunk 16 optimal weight: 0.3980 chunk 18 optimal weight: 0.9980 chunk 5 optimal weight: 0.8980 chunk 2 optimal weight: 3.9990 chunk 8 optimal weight: 0.7980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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 = 0.4044 r_free = 0.4044 target = 0.081815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.066582 restraints weight = 35221.371| |-----------------------------------------------------------------------------| r_work (start): 0.3693 rms_B_bonded: 4.84 r_work: 0.3561 rms_B_bonded: 4.87 restraints_weight: 0.5000 r_work (final): 0.3561 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.2855 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3353 Z= 0.113 Angle : 0.551 9.318 4566 Z= 0.272 Chirality : 0.043 0.133 487 Planarity : 0.004 0.043 594 Dihedral : 4.184 15.809 462 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 5.11 % Favored : 94.65 % Rotamer: Outliers : 1.69 % Allowed : 19.72 % Favored : 78.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.20 (0.42), residues: 411 helix: -1.86 (0.88), residues: 29 sheet: 0.26 (0.47), residues: 129 loop : -0.03 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 PHE 0.013 0.001 PHE A 338 TYR 0.014 0.001 TYR A 369 ARG 0.002 0.000 ARG A 466 Details of bonding type rmsd hydrogen bonds : bond 0.02499 ( 109) hydrogen bonds : angle 5.24614 ( 264) SS BOND : bond 0.00169 ( 6) SS BOND : angle 0.47027 ( 12) covalent geometry : bond 0.00274 ( 3347) covalent geometry : angle 0.55073 ( 4554) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 822 Ramachandran restraints generated. 411 Oldfield, 0 Emsley, 411 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 34 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: L 21 LEU cc_start: 0.9117 (mp) cc_final: 0.8753 (tt) REVERT: A 386 LYS cc_start: 0.8957 (mtpp) cc_final: 0.8681 (mmmt) outliers start: 6 outliers final: 5 residues processed: 37 average time/residue: 1.6784 time to fit residues: 65.1473 Evaluate side-chains 36 residues out of total 355 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 31 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 18 LEU Chi-restraints excluded: chain H residue 71 VAL Chi-restraints excluded: chain H residue 104 ASP Chi-restraints excluded: chain L residue 11 LEU Chi-restraints excluded: chain A residue 336 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 0.9980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 24 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 6 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4035 r_free = 0.4035 target = 0.081446 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3721 r_free = 0.3721 target = 0.066455 restraints weight = 35662.555| |-----------------------------------------------------------------------------| r_work (start): 0.3687 rms_B_bonded: 4.75 r_work: 0.3557 rms_B_bonded: 4.81 restraints_weight: 0.5000 r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7731 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3353 Z= 0.124 Angle : 0.556 10.549 4566 Z= 0.275 Chirality : 0.042 0.132 487 Planarity : 0.004 0.043 594 Dihedral : 4.219 15.783 462 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.24 % Allowed : 4.87 % Favored : 94.89 % Rotamer: Outliers : 1.41 % Allowed : 19.72 % Favored : 78.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -0.19 (0.42), residues: 411 helix: -1.84 (0.88), residues: 29 sheet: 0.32 (0.47), residues: 129 loop : -0.07 (0.40), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 353 HIS 0.002 0.001 HIS A 339 PHE 0.006 0.001 PHE A 377 TYR 0.014 0.001 TYR A 369 ARG 0.001 0.000 ARG A 357 Details of bonding type rmsd hydrogen bonds : bond 0.02525 ( 109) hydrogen bonds : angle 5.24647 ( 264) SS BOND : bond 0.00198 ( 6) SS BOND : angle 0.51120 ( 12) covalent geometry : bond 0.00289 ( 3347) covalent geometry : angle 0.55613 ( 4554) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6577.55 seconds wall clock time: 117 minutes 53.26 seconds (7073.26 seconds total)