Starting phenix.real_space_refine on Wed Jun 4 15:48:22 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7j_28905/06_2025/8f7j_28905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7j_28905/06_2025/8f7j_28905.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.32 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7j_28905/06_2025/8f7j_28905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7j_28905/06_2025/8f7j_28905.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7j_28905/06_2025/8f7j_28905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7j_28905/06_2025/8f7j_28905.cif" } resolution = 4.32 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= 0.043 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 8 5.16 5 C 2135 2.51 5 N 583 2.21 5 O 595 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 10 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 3321 Number of models: 1 Model: "" Number of chains: 1 Chain: "E" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Time building chain proxies: 4.16, per 1000 atoms: 1.25 Number of scatterers: 3321 At special positions: 0 Unit cell: (77.552, 78.6, 79.648, 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 8 16.00 O 595 8.00 N 583 7.00 C 2135 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: 0.84 Conformation dependent library (CDL) restraints added in 406.3 milliseconds 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 788 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 31.4% alpha, 12.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'E' and resid 402 through 411 Processing helix chain 'E' and resid 412 through 420 Processing helix chain 'E' and resid 439 through 444 removed outlier: 3.790A pdb=" N PHE E 443 " --> pdb=" O PRO E 439 " (cutoff:3.500A) Processing helix chain 'E' and resid 462 through 468 removed outlier: 3.588A pdb=" N ILE E 465 " --> pdb=" O PRO E 462 " (cutoff:3.500A) Processing helix chain 'E' and resid 484 through 494 Processing helix chain 'E' and resid 510 through 514 removed outlier: 4.055A pdb=" N TYR E 513 " --> pdb=" O LEU E 510 " (cutoff:3.500A) Processing helix chain 'E' and resid 537 through 541 removed outlier: 3.703A pdb=" N ARG E 541 " --> pdb=" O ASP E 538 " (cutoff:3.500A) Processing helix chain 'E' and resid 559 through 566 removed outlier: 3.788A pdb=" N THR E 563 " --> pdb=" O PRO E 559 " (cutoff:3.500A) Processing helix chain 'E' and resid 632 through 638 removed outlier: 3.749A pdb=" N GLN E 636 " --> pdb=" O ILE E 633 " (cutoff:3.500A) removed outlier: 4.052A pdb=" N HIS E 637 " --> pdb=" O SER E 634 " (cutoff:3.500A) Processing helix chain 'E' and resid 655 through 661 removed outlier: 3.525A pdb=" N LEU E 661 " --> pdb=" O ILE E 658 " (cutoff:3.500A) Processing helix chain 'E' and resid 679 through 684 removed outlier: 3.647A pdb=" N CYS E 684 " --> pdb=" O LEU E 681 " (cutoff:3.500A) Processing helix chain 'E' and resid 701 through 707 removed outlier: 3.953A pdb=" N ILE E 704 " --> pdb=" O PRO E 701 " (cutoff:3.500A) removed outlier: 3.656A pdb=" N LEU E 707 " --> pdb=" O ILE E 704 " (cutoff:3.500A) Processing helix chain 'E' and resid 724 through 730 removed outlier: 3.630A pdb=" N PHE E 728 " --> pdb=" O PRO E 724 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N CYS E 730 " --> pdb=" O GLU E 726 " (cutoff:3.500A) Processing helix chain 'E' and resid 747 through 753 Processing helix chain 'E' and resid 771 through 776 removed outlier: 3.561A pdb=" N CYS E 776 " --> pdb=" O GLU E 772 " (cutoff:3.500A) Processing helix chain 'E' and resid 788 through 793 Processing helix chain 'E' and resid 795 through 808 Processing sheet with id=AA1, first strand: chain 'E' and resid 421 through 422 removed outlier: 6.410A pdb=" N LEU E 428 " --> pdb=" O VAL E 450 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N LYS E 452 " --> pdb=" O LEU E 428 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N LEU E 430 " --> pdb=" O LYS E 452 " (cutoff:3.500A) removed outlier: 6.610A pdb=" N GLU E 454 " --> pdb=" O LEU E 430 " (cutoff:3.500A) removed outlier: 5.915A pdb=" N LEU E 432 " --> pdb=" O GLU E 454 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N LEU E 474 " --> pdb=" O HIS E 499 " (cutoff:3.500A) removed outlier: 7.277A pdb=" N LYS E 501 " --> pdb=" O LEU E 474 " (cutoff:3.500A) removed outlier: 5.954A pdb=" N LEU E 476 " --> pdb=" O LYS E 501 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N LEU E 498 " --> pdb=" O HIS E 522 " (cutoff:3.500A) removed outlier: 7.846A pdb=" N THR E 524 " --> pdb=" O LEU E 498 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ILE E 500 " --> pdb=" O THR E 524 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N LEU E 572 " --> pdb=" O GLU E 597 " (cutoff:3.500A) removed outlier: 7.047A pdb=" N ILE E 599 " --> pdb=" O LEU E 572 " (cutoff:3.500A) removed outlier: 5.985A pdb=" N ILE E 574 " --> pdb=" O ILE E 599 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N LEU E 596 " --> pdb=" O GLU E 618 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N ASP E 620 " --> pdb=" O LEU E 596 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N LEU E 598 " --> pdb=" O ASP E 620 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'E' and resid 459 through 460 removed outlier: 6.483A pdb=" N VAL E 459 " --> pdb=" O LYS E 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 666 through 668 removed outlier: 6.334A pdb=" N TYR E 689 " --> pdb=" O LEU E 667 " (cutoff:3.500A) removed outlier: 6.888A pdb=" N LEU E 690 " --> pdb=" O ALA E 714 " (cutoff:3.500A) removed outlier: 6.311A pdb=" N ILE E 759 " --> pdb=" O VAL E 785 " (cutoff:3.500A) 72 hydrogen bonds defined for protein. 159 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: 1.14 Time building geometry restraints manager: 1.03 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: 1098 1.34 - 1.46: 492 1.46 - 1.58: 1777 1.58 - 1.69: 1 1.69 - 1.81: 10 Bond restraints: 3378 Sorted by residual: bond pdb=" N PRO E 678 " pdb=" CD PRO E 678 " ideal model delta sigma weight residual 1.473 1.417 0.056 1.40e-02 5.10e+03 1.59e+01 bond pdb=" N THR E 412 " pdb=" CA THR E 412 " ideal model delta sigma weight residual 1.453 1.488 -0.034 1.22e-02 6.72e+03 7.93e+00 bond pdb=" N LEU E 420 " pdb=" CA LEU E 420 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.31e-02 5.83e+03 7.20e+00 bond pdb=" N GLN E 404 " pdb=" CA GLN E 404 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.13e+00 bond pdb=" N GLN E 418 " pdb=" CA GLN E 418 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.10e+00 ... (remaining 3373 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.04: 4378 2.04 - 4.07: 174 4.07 - 6.11: 20 6.11 - 8.14: 7 8.14 - 10.18: 1 Bond angle restraints: 4580 Sorted by residual: angle pdb=" CA MET E 590 " pdb=" CB MET E 590 " pdb=" CG MET E 590 " ideal model delta sigma weight residual 114.10 121.55 -7.45 2.00e+00 2.50e-01 1.39e+01 angle pdb=" CB MET E 590 " pdb=" CG MET E 590 " pdb=" SD MET E 590 " ideal model delta sigma weight residual 112.70 122.88 -10.18 3.00e+00 1.11e-01 1.15e+01 angle pdb=" C ASN E 712 " pdb=" CA ASN E 712 " pdb=" CB ASN E 712 " ideal model delta sigma weight residual 109.38 115.00 -5.62 1.80e+00 3.09e-01 9.74e+00 angle pdb=" CA THR E 412 " pdb=" C THR E 412 " pdb=" O THR E 412 " ideal model delta sigma weight residual 121.89 118.24 3.65 1.17e+00 7.31e-01 9.71e+00 angle pdb=" N PRO E 678 " pdb=" CD PRO E 678 " pdb=" CG PRO E 678 " ideal model delta sigma weight residual 103.20 107.81 -4.61 1.50e+00 4.44e-01 9.46e+00 ... (remaining 4575 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.60: 1826 17.60 - 35.19: 204 35.19 - 52.79: 55 52.79 - 70.38: 7 70.38 - 87.98: 2 Dihedral angle restraints: 2094 sinusoidal: 892 harmonic: 1202 Sorted by residual: dihedral pdb=" CA LEU E 468 " pdb=" C LEU E 468 " pdb=" N THR E 469 " pdb=" CA THR E 469 " ideal model delta harmonic sigma weight residual 180.00 -156.22 -23.78 0 5.00e+00 4.00e-02 2.26e+01 dihedral pdb=" CA ILE E 535 " pdb=" C ILE E 535 " pdb=" N VAL E 536 " pdb=" CA VAL E 536 " ideal model delta harmonic sigma weight residual 180.00 157.51 22.49 0 5.00e+00 4.00e-02 2.02e+01 dihedral pdb=" CA THR E 662 " pdb=" C THR E 662 " pdb=" N ASN E 663 " pdb=" CA ASN E 663 " ideal model delta harmonic sigma weight residual -180.00 -160.54 -19.46 0 5.00e+00 4.00e-02 1.51e+01 ... (remaining 2091 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 316 0.038 - 0.076: 167 0.076 - 0.114: 46 0.114 - 0.152: 15 0.152 - 0.190: 5 Chirality restraints: 549 Sorted by residual: chirality pdb=" CA LEU E 405 " pdb=" N LEU E 405 " pdb=" C LEU E 405 " pdb=" CB LEU E 405 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.04e-01 chirality pdb=" CB VAL E 786 " pdb=" CA VAL E 786 " pdb=" CG1 VAL E 786 " pdb=" CG2 VAL E 786 " both_signs ideal model delta sigma weight residual False -2.63 -2.45 -0.18 2.00e-01 2.50e+01 7.87e-01 chirality pdb=" CA LEU E 413 " pdb=" N LEU E 413 " pdb=" C LEU E 413 " pdb=" CB LEU E 413 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.72e-01 ... (remaining 546 not shown) Planarity restraints: 578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE E 677 " 0.047 5.00e-02 4.00e+02 7.28e-02 8.47e+00 pdb=" N PRO E 678 " -0.126 5.00e-02 4.00e+02 pdb=" CA PRO E 678 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO E 678 " 0.041 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE E 490 " 0.006 2.00e-02 2.50e+03 1.83e-02 5.86e+00 pdb=" CG PHE E 490 " -0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE E 490 " 0.020 2.00e-02 2.50e+03 pdb=" CD2 PHE E 490 " 0.020 2.00e-02 2.50e+03 pdb=" CE1 PHE E 490 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE E 490 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE E 490 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU E 746 " 0.030 5.00e-02 4.00e+02 4.61e-02 3.41e+00 pdb=" N PRO E 747 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO E 747 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO E 747 " 0.025 5.00e-02 4.00e+02 ... (remaining 575 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 833 2.81 - 3.33: 3140 3.33 - 3.85: 5722 3.85 - 4.38: 7130 4.38 - 4.90: 11101 Nonbonded interactions: 27926 Sorted by model distance: nonbonded pdb=" O VAL E 591 " pdb=" ND2 ASN E 615 " model vdw 2.282 3.120 nonbonded pdb=" O LEU E 476 " pdb=" N LYS E 501 " model vdw 2.300 3.120 nonbonded pdb=" OH TYR E 689 " pdb=" OE1 GLN E 711 " model vdw 2.315 3.040 nonbonded pdb=" O GLN E 560 " pdb=" OG1 THR E 563 " model vdw 2.328 3.040 nonbonded pdb=" O LEU E 790 " pdb=" OG1 THR E 793 " model vdw 2.328 3.040 ... (remaining 27921 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.560 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 15.530 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 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:3.250 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.590 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3391 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 : 0.005 0.121 3378 Z= 0.281 Angle : 0.925 10.180 4580 Z= 0.541 Chirality : 0.051 0.190 549 Planarity : 0.006 0.073 578 Dihedral : 15.435 87.977 1306 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 15.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.26 % Allowed : 18.25 % Favored : 81.48 % 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: -3.18 (0.39), residues: 405 helix: -2.98 (0.38), residues: 115 sheet: -2.33 (0.78), residues: 54 loop : -1.56 (0.39), residues: 236 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP E 475 HIS 0.011 0.002 HIS E 694 PHE 0.039 0.003 PHE E 490 TYR 0.012 0.002 TYR E 477 ARG 0.005 0.001 ARG E 419 Details of bonding type rmsd hydrogen bonds : bond 0.16674 ( 72) hydrogen bonds : angle 8.39654 ( 159) covalent geometry : bond 0.00505 ( 3378) covalent geometry : angle 0.92489 ( 4580) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 516 LYS cc_start: 0.7151 (mttt) cc_final: 0.6670 (tptp) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.1855 time to fit residues: 20.8513 Evaluate side-chains 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 16 optimal weight: 9.9990 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.0000 chunk 31 optimal weight: 0.7980 chunk 12 optimal weight: 10.0000 chunk 19 optimal weight: 3.9990 chunk 23 optimal weight: 6.9990 chunk 36 optimal weight: 0.8980 chunk 11 optimal weight: 0.9990 overall best weight: 0.6786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 560 GLN E 585 ASN E 741 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4950 r_free = 0.4950 target = 0.188125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.175884 restraints weight = 17619.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4813 r_free = 0.4813 target = 0.177471 restraints weight = 14168.062| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.178491 restraints weight = 11664.389| |-----------------------------------------------------------------------------| r_work (final): 0.4797 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3709 moved from start: 0.4097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3378 Z= 0.146 Angle : 0.678 9.180 4580 Z= 0.343 Chirality : 0.045 0.152 549 Planarity : 0.005 0.042 578 Dihedral : 5.285 19.886 439 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 0.00 % Allowed : 3.17 % Favored : 96.83 % 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: -3.41 (0.38), residues: 405 helix: -2.77 (0.38), residues: 136 sheet: -1.99 (0.88), residues: 45 loop : -1.96 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP E 647 HIS 0.004 0.001 HIS E 522 PHE 0.013 0.002 PHE E 611 TYR 0.024 0.002 TYR E 477 ARG 0.007 0.001 ARG E 492 Details of bonding type rmsd hydrogen bonds : bond 0.04206 ( 72) hydrogen bonds : angle 6.27107 ( 159) covalent geometry : bond 0.00322 ( 3378) covalent geometry : angle 0.67836 ( 4580) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.383 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 410 GLU cc_start: 0.7687 (tp30) cc_final: 0.7451 (tp30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1437 time to fit residues: 10.6224 Evaluate side-chains 40 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.378 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 17 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.0040 chunk 16 optimal weight: 5.9990 chunk 1 optimal weight: 5.9990 chunk 34 optimal weight: 0.1980 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 overall best weight: 0.9794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 608 HIS E 708 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4928 r_free = 0.4928 target = 0.187026 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 69)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.173610 restraints weight = 17352.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4794 r_free = 0.4794 target = 0.175100 restraints weight = 13272.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.176952 restraints weight = 10828.470| |-----------------------------------------------------------------------------| r_work (final): 0.4779 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3977 moved from start: 0.5391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3378 Z= 0.142 Angle : 0.636 6.118 4580 Z= 0.323 Chirality : 0.045 0.184 549 Planarity : 0.005 0.044 578 Dihedral : 4.959 21.225 439 Min Nonbonded Distance : 2.564 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % 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: -3.32 (0.39), residues: 405 helix: -2.60 (0.39), residues: 135 sheet: -2.28 (0.77), residues: 45 loop : -1.90 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP E 647 HIS 0.003 0.001 HIS E 431 PHE 0.014 0.002 PHE E 611 TYR 0.016 0.002 TYR E 477 ARG 0.003 0.000 ARG E 419 Details of bonding type rmsd hydrogen bonds : bond 0.03465 ( 72) hydrogen bonds : angle 5.71224 ( 159) covalent geometry : bond 0.00299 ( 3378) covalent geometry : angle 0.63593 ( 4580) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 647 TRP cc_start: 0.6657 (p90) cc_final: 0.6272 (p90) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1175 time to fit residues: 7.8296 Evaluate side-chains 37 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 37 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 5.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 20 optimal weight: 2.9990 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 7 optimal weight: 0.7980 chunk 16 optimal weight: 5.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- 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 = 0.4905 r_free = 0.4905 target = 0.184146 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.4732 r_free = 0.4732 target = 0.170295 restraints weight = 17311.105| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.172217 restraints weight = 13626.276| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.173984 restraints weight = 11170.865| |-----------------------------------------------------------------------------| r_work (final): 0.4750 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4150 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 3378 Z= 0.140 Angle : 0.642 5.692 4580 Z= 0.324 Chirality : 0.044 0.163 549 Planarity : 0.005 0.039 578 Dihedral : 4.898 19.201 439 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 18.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.35 (0.39), residues: 405 helix: -2.55 (0.39), residues: 136 sheet: -2.19 (0.83), residues: 45 loop : -1.99 (0.40), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP E 647 HIS 0.004 0.001 HIS E 608 PHE 0.010 0.002 PHE E 682 TYR 0.025 0.002 TYR E 513 ARG 0.006 0.001 ARG E 492 Details of bonding type rmsd hydrogen bonds : bond 0.03180 ( 72) hydrogen bonds : angle 5.72365 ( 159) covalent geometry : bond 0.00318 ( 3378) covalent geometry : angle 0.64233 ( 4580) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 433 PHE cc_start: 0.5031 (t80) cc_final: 0.4824 (t80) REVERT: E 471 LEU cc_start: 0.6514 (tp) cc_final: 0.6302 (tp) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1268 time to fit residues: 8.8959 Evaluate side-chains 41 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 41 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 8.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 5 optimal weight: 0.9990 chunk 8 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 overall best weight: 1.1586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 494 ASN E 711 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4897 r_free = 0.4897 target = 0.182328 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4734 r_free = 0.4734 target = 0.169636 restraints weight = 17263.526| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.171449 restraints weight = 13306.121| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4783 r_free = 0.4783 target = 0.172974 restraints weight = 10578.405| |-----------------------------------------------------------------------------| r_work (final): 0.4780 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4158 moved from start: 0.7329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3378 Z= 0.121 Angle : 0.607 8.212 4580 Z= 0.310 Chirality : 0.043 0.134 549 Planarity : 0.004 0.038 578 Dihedral : 4.761 18.413 439 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % 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: -3.38 (0.39), residues: 405 helix: -2.71 (0.38), residues: 137 sheet: -2.22 (0.71), residues: 56 loop : -1.85 (0.42), residues: 212 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 647 HIS 0.002 0.000 HIS E 522 PHE 0.010 0.001 PHE E 611 TYR 0.026 0.002 TYR E 513 ARG 0.002 0.000 ARG E 688 Details of bonding type rmsd hydrogen bonds : bond 0.03179 ( 72) hydrogen bonds : angle 5.59599 ( 159) covalent geometry : bond 0.00259 ( 3378) covalent geometry : angle 0.60652 ( 4580) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.357 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 433 PHE cc_start: 0.5025 (t80) cc_final: 0.4710 (t80) REVERT: E 471 LEU cc_start: 0.6369 (tp) cc_final: 0.6067 (tp) REVERT: E 658 ILE cc_start: 0.5455 (tp) cc_final: 0.5056 (mm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1328 time to fit residues: 8.8745 Evaluate side-chains 40 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 40 time to evaluate : 0.359 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 3.9990 chunk 13 optimal weight: 0.9980 chunk 24 optimal weight: 0.8980 chunk 5 optimal weight: 0.8980 chunk 6 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 16 optimal weight: 2.9990 chunk 12 optimal weight: 9.9990 overall best weight: 1.7584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 HIS ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4826 r_free = 0.4826 target = 0.176468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.162918 restraints weight = 17588.851| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.164733 restraints weight = 13346.113| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.166590 restraints weight = 10562.456| |-----------------------------------------------------------------------------| r_work (final): 0.4686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4481 moved from start: 0.8490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 3378 Z= 0.161 Angle : 0.702 6.496 4580 Z= 0.350 Chirality : 0.044 0.167 549 Planarity : 0.005 0.040 578 Dihedral : 5.150 17.930 439 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 20.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: -3.41 (0.40), residues: 405 helix: -2.71 (0.39), residues: 135 sheet: -2.48 (0.63), residues: 72 loop : -1.69 (0.44), residues: 198 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP E 647 HIS 0.006 0.001 HIS E 478 PHE 0.013 0.002 PHE E 699 TYR 0.016 0.002 TYR E 513 ARG 0.005 0.001 ARG E 688 Details of bonding type rmsd hydrogen bonds : bond 0.03416 ( 72) hydrogen bonds : angle 5.68041 ( 159) covalent geometry : bond 0.00360 ( 3378) covalent geometry : angle 0.70199 ( 4580) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 48 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 477 TYR cc_start: 0.7285 (m-80) cc_final: 0.7072 (m-10) REVERT: E 590 MET cc_start: 0.3723 (mmp) cc_final: 0.3507 (mmm) outliers start: 0 outliers final: 0 residues processed: 48 average time/residue: 0.1264 time to fit residues: 8.1440 Evaluate side-chains 33 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 33 time to evaluate : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 7.9990 chunk 31 optimal weight: 10.0000 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 10.0000 chunk 5 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 3.9990 chunk 13 optimal weight: 9.9990 chunk 19 optimal weight: 7.9990 chunk 34 optimal weight: 0.3980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 HIS ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.176836 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 75)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.164884 restraints weight = 17317.170| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4705 r_free = 0.4705 target = 0.166388 restraints weight = 13435.427| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4728 r_free = 0.4728 target = 0.167908 restraints weight = 10738.764| |-----------------------------------------------------------------------------| r_work (final): 0.4723 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4314 moved from start: 0.8802 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3378 Z= 0.113 Angle : 0.592 6.351 4580 Z= 0.304 Chirality : 0.042 0.125 549 Planarity : 0.004 0.033 578 Dihedral : 4.789 17.279 439 Min Nonbonded Distance : 2.441 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: -3.23 (0.41), residues: 405 helix: -2.61 (0.40), residues: 135 sheet: -1.97 (0.67), residues: 67 loop : -1.75 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 475 HIS 0.003 0.001 HIS E 499 PHE 0.010 0.001 PHE E 611 TYR 0.009 0.002 TYR E 513 ARG 0.002 0.000 ARG E 688 Details of bonding type rmsd hydrogen bonds : bond 0.02949 ( 72) hydrogen bonds : angle 5.37863 ( 159) covalent geometry : bond 0.00247 ( 3378) covalent geometry : angle 0.59210 ( 4580) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 410 GLU cc_start: 0.6936 (tm-30) cc_final: 0.5501 (tm-30) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1403 time to fit residues: 9.4205 Evaluate side-chains 38 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 38 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 19 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 8 optimal weight: 8.9990 chunk 10 optimal weight: 0.9980 chunk 5 optimal weight: 4.9990 chunk 1 optimal weight: 0.7980 chunk 15 optimal weight: 0.9990 chunk 36 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 23 optimal weight: 8.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4829 r_free = 0.4829 target = 0.176606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.4672 r_free = 0.4672 target = 0.163764 restraints weight = 17403.520| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.165506 restraints weight = 13759.580| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.167101 restraints weight = 11048.131| |-----------------------------------------------------------------------------| r_work (final): 0.4711 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4355 moved from start: 0.9311 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3378 Z= 0.114 Angle : 0.602 6.333 4580 Z= 0.308 Chirality : 0.043 0.159 549 Planarity : 0.005 0.036 578 Dihedral : 4.684 16.605 439 Min Nonbonded Distance : 2.418 Molprobity Statistics. All-atom Clashscore : 16.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -3.23 (0.41), residues: 405 helix: -2.70 (0.39), residues: 135 sheet: -1.97 (0.68), residues: 65 loop : -1.70 (0.45), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.004 TRP E 475 HIS 0.019 0.001 HIS E 499 PHE 0.010 0.001 PHE E 611 TYR 0.006 0.001 TYR E 477 ARG 0.002 0.000 ARG E 492 Details of bonding type rmsd hydrogen bonds : bond 0.02926 ( 72) hydrogen bonds : angle 5.45452 ( 159) covalent geometry : bond 0.00249 ( 3378) covalent geometry : angle 0.60201 ( 4580) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 521 LEU cc_start: 0.5637 (mt) cc_final: 0.5406 (mt) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1295 time to fit residues: 8.4556 Evaluate side-chains 36 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 38 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 22 optimal weight: 3.9990 chunk 12 optimal weight: 0.5980 chunk 27 optimal weight: 0.6980 chunk 13 optimal weight: 8.9990 chunk 32 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 37 optimal weight: 0.6980 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 = 0.4812 r_free = 0.4812 target = 0.175449 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4662 r_free = 0.4662 target = 0.163244 restraints weight = 17448.285| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4684 r_free = 0.4684 target = 0.164752 restraints weight = 13848.598| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4701 r_free = 0.4701 target = 0.166107 restraints weight = 11135.612| |-----------------------------------------------------------------------------| r_work (final): 0.4694 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4360 moved from start: 0.9605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 3378 Z= 0.112 Angle : 0.586 6.614 4580 Z= 0.299 Chirality : 0.043 0.172 549 Planarity : 0.005 0.035 578 Dihedral : 4.622 16.118 439 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.26 % Favored : 99.74 % 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: -3.16 (0.41), residues: 405 helix: -2.64 (0.40), residues: 135 sheet: -2.05 (0.66), residues: 69 loop : -1.58 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.004 TRP E 475 HIS 0.023 0.002 HIS E 499 PHE 0.010 0.001 PHE E 611 TYR 0.022 0.002 TYR E 513 ARG 0.002 0.000 ARG E 492 Details of bonding type rmsd hydrogen bonds : bond 0.02749 ( 72) hydrogen bonds : angle 5.20000 ( 159) covalent geometry : bond 0.00241 ( 3378) covalent geometry : angle 0.58643 ( 4580) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 521 LEU cc_start: 0.5926 (mt) cc_final: 0.5723 (mt) REVERT: E 658 ILE cc_start: 0.4875 (tp) cc_final: 0.4433 (mm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1299 time to fit residues: 8.4946 Evaluate side-chains 36 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 39 optimal weight: 4.9990 chunk 38 optimal weight: 9.9990 chunk 10 optimal weight: 5.9990 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 12 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.8980 overall best weight: 0.7138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.174723 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.162684 restraints weight = 17460.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.164175 restraints weight = 13788.824| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.165582 restraints weight = 11036.364| |-----------------------------------------------------------------------------| r_work (final): 0.4684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4360 moved from start: 0.9962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3378 Z= 0.107 Angle : 0.587 6.930 4580 Z= 0.298 Chirality : 0.042 0.131 549 Planarity : 0.004 0.036 578 Dihedral : 4.533 15.402 439 Min Nonbonded Distance : 2.380 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % Rotamer: Outliers : 0.00 % Allowed : 0.53 % Favored : 99.47 % 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: -3.42 (0.40), residues: 405 helix: -2.80 (0.38), residues: 143 sheet: -1.94 (0.68), residues: 69 loop : -1.83 (0.43), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.004 TRP E 475 HIS 0.017 0.002 HIS E 499 PHE 0.010 0.001 PHE E 611 TYR 0.020 0.001 TYR E 513 ARG 0.002 0.000 ARG E 419 Details of bonding type rmsd hydrogen bonds : bond 0.02763 ( 72) hydrogen bonds : angle 5.10406 ( 159) covalent geometry : bond 0.00237 ( 3378) covalent geometry : angle 0.58707 ( 4580) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 658 ILE cc_start: 0.4861 (tp) cc_final: 0.4415 (mm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1326 time to fit residues: 8.9907 Evaluate side-chains 36 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 36 time to evaluate : 0.382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 11 optimal weight: 1.9990 chunk 5 optimal weight: 0.1980 chunk 16 optimal weight: 0.9990 chunk 36 optimal weight: 0.9990 chunk 20 optimal weight: 0.0060 chunk 13 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 2 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 39 optimal weight: 6.9990 chunk 24 optimal weight: 3.9990 overall best weight: 0.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 560 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN E 758 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4808 r_free = 0.4808 target = 0.175024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.162849 restraints weight = 16886.687| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4676 r_free = 0.4676 target = 0.164488 restraints weight = 13318.071| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.166088 restraints weight = 10639.214| |-----------------------------------------------------------------------------| r_work (final): 0.4692 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4329 moved from start: 1.0158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 3378 Z= 0.109 Angle : 0.617 6.820 4580 Z= 0.311 Chirality : 0.042 0.130 549 Planarity : 0.004 0.034 578 Dihedral : 4.540 15.205 439 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 16.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.26 % Allowed : 0.00 % Favored : 99.74 % 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: -3.44 (0.40), residues: 405 helix: -2.76 (0.38), residues: 144 sheet: -1.91 (0.67), residues: 69 loop : -1.90 (0.43), residues: 192 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 475 HIS 0.017 0.002 HIS E 499 PHE 0.010 0.001 PHE E 611 TYR 0.019 0.001 TYR E 513 ARG 0.003 0.000 ARG E 419 Details of bonding type rmsd hydrogen bonds : bond 0.02575 ( 72) hydrogen bonds : angle 5.13882 ( 159) covalent geometry : bond 0.00243 ( 3378) covalent geometry : angle 0.61705 ( 4580) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1777.04 seconds wall clock time: 31 minutes 24.71 seconds (1884.71 seconds total)