Starting phenix.real_space_refine on Fri Aug 22 13:38:02 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7j_28905/08_2025/8f7j_28905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7j_28905/08_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 { model { file = "/net/cci-nas-00/data/ceres_data/8f7j_28905/08_2025/8f7j_28905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7j_28905/08_2025/8f7j_28905.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8f7j_28905/08_2025/8f7j_28905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7j_28905/08_2025/8f7j_28905.map" } resolution = 4.32 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/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: 1.06, per 1000 atoms: 0.32 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: 0.18 Conformation dependent library (CDL) restraints added in 98.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 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: 0.08 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: 0.37 Time building geometry restraints manager: 0.28 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: 5.590 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: 0.080 Check model and map are aligned: 0.010 Set scattering table: 0.000 Process input model: 4.940 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.060 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 11.710 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.005 0.001 ARG E 419 TYR 0.012 0.002 TYR E 477 PHE 0.039 0.003 PHE E 490 TRP 0.032 0.003 TRP E 475 HIS 0.011 0.002 HIS E 694 Details of bonding type rmsd covalent geometry : bond 0.00505 ( 3378) covalent geometry : angle 0.92489 ( 4580) hydrogen bonds : bond 0.16674 ( 72) hydrogen bonds : angle 8.39654 ( 159) *********************** 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 : 0.127 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: 0.0734 time to fit residues: 8.2770 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 : 0.173 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.5980 chunk 26 optimal weight: 0.8980 chunk 2 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 31 optimal weight: 0.0570 chunk 25 optimal weight: 8.9990 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 overall best weight: 1.1102 ------------------------------------------------------------------------------- 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 708 GLN E 741 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4941 r_free = 0.4941 target = 0.187219 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4781 r_free = 0.4781 target = 0.173988 restraints weight = 18178.653| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.176067 restraints weight = 14259.618| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4825 r_free = 0.4825 target = 0.177631 restraints weight = 11346.290| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 43)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.178774 restraints weight = 9410.573| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4848 r_free = 0.4848 target = 0.179501 restraints weight = 8037.884| |-----------------------------------------------------------------------------| r_work (final): 0.4819 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3798 moved from start: 0.4320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3378 Z= 0.153 Angle : 0.693 9.345 4580 Z= 0.350 Chirality : 0.045 0.156 549 Planarity : 0.006 0.047 578 Dihedral : 5.325 19.892 439 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 19.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.38), residues: 405 helix: -2.82 (0.38), residues: 136 sheet: -1.96 (0.88), residues: 45 loop : -2.01 (0.38), residues: 224 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 492 TYR 0.023 0.003 TYR E 477 PHE 0.013 0.002 PHE E 611 TRP 0.045 0.003 TRP E 647 HIS 0.004 0.001 HIS E 522 Details of bonding type rmsd covalent geometry : bond 0.00336 ( 3378) covalent geometry : angle 0.69284 ( 4580) hydrogen bonds : bond 0.04174 ( 72) hydrogen bonds : angle 6.32176 ( 159) *********************** 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 : 0.104 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 ASN cc_start: 0.8475 (m-40) cc_final: 0.8273 (m110) REVERT: E 410 GLU cc_start: 0.7815 (tp30) cc_final: 0.7545 (tp30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.0667 time to fit residues: 4.8855 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 : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 24 optimal weight: 0.1980 chunk 17 optimal weight: 0.8980 chunk 32 optimal weight: 0.0170 chunk 12 optimal weight: 20.0000 chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 0.7980 chunk 20 optimal weight: 0.7980 chunk 1 optimal weight: 0.3980 chunk 2 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 0.9980 overall best weight: 0.4418 ------------------------------------------------------------------------------- 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 = 0.4939 r_free = 0.4939 target = 0.188486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4778 r_free = 0.4778 target = 0.175043 restraints weight = 17785.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 48)----------------| | r_work = 0.4804 r_free = 0.4804 target = 0.176920 restraints weight = 13697.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.4824 r_free = 0.4824 target = 0.178663 restraints weight = 10952.407| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 60)----------------| | r_work = 0.4840 r_free = 0.4840 target = 0.180132 restraints weight = 9009.823| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 42)----------------| | r_work = 0.4851 r_free = 0.4851 target = 0.180984 restraints weight = 7598.385| |-----------------------------------------------------------------------------| r_work (final): 0.4825 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3800 moved from start: 0.5147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3378 Z= 0.116 Angle : 0.617 6.845 4580 Z= 0.312 Chirality : 0.045 0.173 549 Planarity : 0.004 0.042 578 Dihedral : 4.870 21.413 439 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 16.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.27 (0.39), residues: 405 helix: -2.55 (0.40), residues: 135 sheet: -2.24 (0.78), residues: 45 loop : -1.88 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG E 419 TYR 0.017 0.002 TYR E 477 PHE 0.013 0.001 PHE E 611 TRP 0.024 0.002 TRP E 647 HIS 0.001 0.000 HIS E 522 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3378) covalent geometry : angle 0.61661 ( 4580) hydrogen bonds : bond 0.03451 ( 72) hydrogen bonds : angle 5.60954 ( 159) *********************** 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 : 0.143 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 471 LEU cc_start: 0.6726 (tp) cc_final: 0.6523 (tp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0680 time to fit residues: 4.2821 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 : 0.168 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 8 optimal weight: 0.5980 chunk 2 optimal weight: 1.9990 chunk 12 optimal weight: 9.9990 chunk 39 optimal weight: 9.9990 chunk 19 optimal weight: 5.9990 chunk 13 optimal weight: 0.3980 chunk 28 optimal weight: 7.9990 chunk 18 optimal weight: 0.3980 chunk 0 optimal weight: 6.9990 chunk 27 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 608 HIS E 649 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4921 r_free = 0.4921 target = 0.186317 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 64)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.171961 restraints weight = 17599.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4775 r_free = 0.4775 target = 0.173924 restraints weight = 13816.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4801 r_free = 0.4801 target = 0.175965 restraints weight = 11200.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4820 r_free = 0.4820 target = 0.177497 restraints weight = 9184.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4836 r_free = 0.4836 target = 0.178791 restraints weight = 7742.327| |-----------------------------------------------------------------------------| r_work (final): 0.4808 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3951 moved from start: 0.5989 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3378 Z= 0.119 Angle : 0.594 5.469 4580 Z= 0.302 Chirality : 0.043 0.167 549 Planarity : 0.004 0.035 578 Dihedral : 4.737 19.801 439 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 17.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 3.97 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.26 (0.40), residues: 405 helix: -2.46 (0.40), residues: 135 sheet: -2.30 (0.81), residues: 45 loop : -1.93 (0.40), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 545 TYR 0.025 0.002 TYR E 513 PHE 0.009 0.001 PHE E 611 TRP 0.039 0.003 TRP E 647 HIS 0.002 0.001 HIS E 522 Details of bonding type rmsd covalent geometry : bond 0.00267 ( 3378) covalent geometry : angle 0.59397 ( 4580) hydrogen bonds : bond 0.02974 ( 72) hydrogen bonds : angle 5.48917 ( 159) *********************** 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 55 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.141 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 471 LEU cc_start: 0.6679 (tp) cc_final: 0.6430 (tp) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.0661 time to fit residues: 4.5048 Evaluate side-chains 39 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.141 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 19 optimal weight: 9.9990 chunk 25 optimal weight: 0.4980 chunk 30 optimal weight: 0.0050 chunk 3 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 38 optimal weight: 20.0000 chunk 7 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.3000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 711 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4885 r_free = 0.4885 target = 0.181931 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.169252 restraints weight = 17136.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4760 r_free = 0.4760 target = 0.171050 restraints weight = 13436.868| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4782 r_free = 0.4782 target = 0.172797 restraints weight = 10831.542| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4798 r_free = 0.4798 target = 0.174120 restraints weight = 8868.981| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 43)----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.175225 restraints weight = 7341.043| |-----------------------------------------------------------------------------| r_work (final): 0.4810 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4034 moved from start: 0.7224 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= 0.133 Angle : 0.642 6.001 4580 Z= 0.324 Chirality : 0.045 0.137 549 Planarity : 0.005 0.038 578 Dihedral : 4.828 18.257 439 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 17.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.39), residues: 405 helix: -2.77 (0.38), residues: 137 sheet: -2.74 (0.74), residues: 51 loop : -1.80 (0.42), residues: 217 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG E 496 TYR 0.018 0.002 TYR E 513 PHE 0.010 0.002 PHE E 682 TRP 0.017 0.001 TRP E 647 HIS 0.003 0.001 HIS E 568 Details of bonding type rmsd covalent geometry : bond 0.00292 ( 3378) covalent geometry : angle 0.64174 ( 4580) hydrogen bonds : bond 0.03300 ( 72) hydrogen bonds : angle 5.56550 ( 159) *********************** 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 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.108 Fit side-chains revert: symmetry clash REVERT: E 491 LEU cc_start: 0.8112 (mt) cc_final: 0.7872 (mm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0626 time to fit residues: 4.0223 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 : 0.134 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 16 optimal weight: 0.6980 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 36 optimal weight: 0.0060 chunk 0 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 1.9990 chunk 33 optimal weight: 1.9990 overall best weight: 1.5402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 494 ASN ** 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 = 0.4827 r_free = 0.4827 target = 0.177690 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4683 r_free = 0.4683 target = 0.165081 restraints weight = 17451.709| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.167181 restraints weight = 13267.261| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4729 r_free = 0.4729 target = 0.168432 restraints weight = 10389.961| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 58)----------------| | r_work = 0.4749 r_free = 0.4749 target = 0.170371 restraints weight = 8517.835| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4759 r_free = 0.4759 target = 0.171198 restraints weight = 6906.698| |-----------------------------------------------------------------------------| r_work (final): 0.4757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4191 moved from start: 0.8180 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= 0.151 Angle : 0.657 6.425 4580 Z= 0.332 Chirality : 0.044 0.152 549 Planarity : 0.005 0.043 578 Dihedral : 4.993 17.658 439 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.47 (0.40), residues: 405 helix: -2.82 (0.37), residues: 136 sheet: -2.54 (0.69), residues: 61 loop : -1.75 (0.44), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG E 492 TYR 0.025 0.002 TYR E 513 PHE 0.011 0.002 PHE E 728 TRP 0.036 0.003 TRP E 647 HIS 0.003 0.001 HIS E 568 Details of bonding type rmsd covalent geometry : bond 0.00323 ( 3378) covalent geometry : angle 0.65738 ( 4580) hydrogen bonds : bond 0.03266 ( 72) hydrogen bonds : angle 5.64851 ( 159) *********************** 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 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.095 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 471 LEU cc_start: 0.6501 (tp) cc_final: 0.6275 (tp) REVERT: E 599 ILE cc_start: 0.5338 (mm) cc_final: 0.5127 (mm) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0535 time to fit residues: 3.3882 Evaluate side-chains 35 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 35 time to evaluate : 0.124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 10.0000 chunk 8 optimal weight: 2.9990 chunk 13 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 25 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 4 optimal weight: 0.8980 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 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 = 0.4808 r_free = 0.4808 target = 0.176053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.161495 restraints weight = 17297.196| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 52)----------------| | r_work = 0.4669 r_free = 0.4669 target = 0.163278 restraints weight = 13902.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4685 r_free = 0.4685 target = 0.164569 restraints weight = 11387.616| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.4699 r_free = 0.4699 target = 0.165889 restraints weight = 9573.770| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.167147 restraints weight = 8097.534| |-----------------------------------------------------------------------------| r_work (final): 0.4715 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4271 moved from start: 0.8590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3378 Z= 0.125 Angle : 0.612 6.510 4580 Z= 0.308 Chirality : 0.042 0.129 549 Planarity : 0.005 0.045 578 Dihedral : 4.766 17.388 439 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 15.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.26 (0.41), residues: 405 helix: -2.68 (0.39), residues: 136 sheet: -2.06 (0.68), residues: 68 loop : -1.70 (0.45), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG E 496 TYR 0.023 0.002 TYR E 513 PHE 0.011 0.002 PHE E 611 TRP 0.028 0.002 TRP E 647 HIS 0.005 0.001 HIS E 568 Details of bonding type rmsd covalent geometry : bond 0.00280 ( 3378) covalent geometry : angle 0.61165 ( 4580) hydrogen bonds : bond 0.02753 ( 72) hydrogen bonds : angle 5.38977 ( 159) *********************** 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 54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 471 LEU cc_start: 0.6376 (tp) cc_final: 0.6103 (tp) REVERT: E 658 ILE cc_start: 0.5074 (tp) cc_final: 0.4720 (mm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0583 time to fit residues: 4.0538 Evaluate side-chains 39 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.136 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 36 optimal weight: 0.1980 chunk 20 optimal weight: 9.9990 chunk 18 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 14 optimal weight: 5.9990 chunk 37 optimal weight: 0.0770 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 overall best weight: 0.5940 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 560 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4806 r_free = 0.4806 target = 0.176392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4652 r_free = 0.4652 target = 0.164118 restraints weight = 17844.975| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4681 r_free = 0.4681 target = 0.166012 restraints weight = 13709.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 46)----------------| | r_work = 0.4703 r_free = 0.4703 target = 0.167661 restraints weight = 10739.761| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4718 r_free = 0.4718 target = 0.168831 restraints weight = 8524.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4731 r_free = 0.4731 target = 0.169907 restraints weight = 6933.474| |-----------------------------------------------------------------------------| r_work (final): 0.4728 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4157 moved from start: 0.8776 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 3378 Z= 0.105 Angle : 0.580 6.650 4580 Z= 0.293 Chirality : 0.042 0.150 549 Planarity : 0.005 0.044 578 Dihedral : 4.481 16.753 439 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.12 (0.41), residues: 405 helix: -2.51 (0.41), residues: 136 sheet: -1.77 (0.70), residues: 63 loop : -1.77 (0.44), residues: 206 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 496 TYR 0.006 0.001 TYR E 534 PHE 0.008 0.001 PHE E 611 TRP 0.023 0.002 TRP E 647 HIS 0.005 0.001 HIS E 568 Details of bonding type rmsd covalent geometry : bond 0.00231 ( 3378) covalent geometry : angle 0.57981 ( 4580) hydrogen bonds : bond 0.02678 ( 72) hydrogen bonds : angle 5.13196 ( 159) *********************** 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 54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.158 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 599 ILE cc_start: 0.5363 (mm) cc_final: 0.5132 (mm) REVERT: E 658 ILE cc_start: 0.5164 (tp) cc_final: 0.4744 (mm) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.0524 time to fit residues: 3.6327 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 : 0.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 3.9990 chunk 26 optimal weight: 8.9990 chunk 36 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 3 optimal weight: 3.9990 chunk 28 optimal weight: 2.9990 chunk 1 optimal weight: 5.9990 chunk 39 optimal weight: 6.9990 chunk 20 optimal weight: 0.0970 chunk 5 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 overall best weight: 2.4184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 HIS ** E 499 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4733 r_free = 0.4733 target = 0.169111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.156823 restraints weight = 17495.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.4606 r_free = 0.4606 target = 0.158472 restraints weight = 13234.964| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4625 r_free = 0.4625 target = 0.159950 restraints weight = 10504.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 57)----------------| | r_work = 0.4638 r_free = 0.4638 target = 0.161389 restraints weight = 8631.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 46)----------------| | r_work = 0.4649 r_free = 0.4649 target = 0.162287 restraints weight = 7218.492| |-----------------------------------------------------------------------------| r_work (final): 0.4647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4555 moved from start: 1.0087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.050 3378 Z= 0.217 Angle : 0.812 7.580 4580 Z= 0.416 Chirality : 0.048 0.213 549 Planarity : 0.006 0.051 578 Dihedral : 5.886 21.745 439 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 26.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.88 % Favored : 90.12 % Rotamer: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.32 (0.41), residues: 405 helix: -2.76 (0.39), residues: 136 sheet: -2.15 (0.67), residues: 68 loop : -1.69 (0.46), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 496 TYR 0.017 0.002 TYR E 477 PHE 0.021 0.003 PHE E 611 TRP 0.028 0.003 TRP E 647 HIS 0.008 0.002 HIS E 431 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 3378) covalent geometry : angle 0.81225 ( 4580) hydrogen bonds : bond 0.03930 ( 72) hydrogen bonds : angle 6.11007 ( 159) *********************** 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 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 410 GLU cc_start: 0.7161 (tm-30) cc_final: 0.5987 (tm-30) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.0448 time to fit residues: 2.9784 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 : 0.089 ------------------------------------------------------------------------------- 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: 0.7980 chunk 38 optimal weight: 7.9990 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 17 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 26 optimal weight: 9.9990 chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 6.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 HIS ** E 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 709 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 758 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4752 r_free = 0.4752 target = 0.171596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4584 r_free = 0.4584 target = 0.156473 restraints weight = 17068.167| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4610 r_free = 0.4610 target = 0.158346 restraints weight = 13255.680| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4629 r_free = 0.4629 target = 0.159993 restraints weight = 10703.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4641 r_free = 0.4641 target = 0.160935 restraints weight = 9001.208| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 40)----------------| | r_work = 0.4654 r_free = 0.4654 target = 0.162234 restraints weight = 7848.584| |-----------------------------------------------------------------------------| r_work (final): 0.4662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4461 moved from start: 1.0132 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3378 Z= 0.121 Angle : 0.619 6.797 4580 Z= 0.318 Chirality : 0.043 0.148 549 Planarity : 0.005 0.036 578 Dihedral : 4.976 16.690 439 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.17 % Favored : 93.83 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.25 (0.41), residues: 405 helix: -2.68 (0.39), residues: 135 sheet: -1.72 (0.70), residues: 63 loop : -1.85 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 496 TYR 0.008 0.001 TYR E 477 PHE 0.011 0.002 PHE E 611 TRP 0.031 0.003 TRP E 411 HIS 0.003 0.001 HIS E 431 Details of bonding type rmsd covalent geometry : bond 0.00271 ( 3378) covalent geometry : angle 0.61867 ( 4580) hydrogen bonds : bond 0.02983 ( 72) hydrogen bonds : angle 5.57598 ( 159) ********************** 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 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 599 ILE cc_start: 0.5683 (mm) cc_final: 0.5404 (mm) REVERT: E 704 ILE cc_start: 0.5683 (tp) cc_final: 0.5349 (tp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.0509 time to fit residues: 3.3187 Evaluate side-chains 39 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 39 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 34 optimal weight: 0.2980 chunk 11 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 20 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 chunk 13 optimal weight: 9.9990 chunk 17 optimal weight: 9.9990 chunk 7 optimal weight: 3.9990 chunk 16 optimal weight: 10.0000 chunk 32 optimal weight: 0.0870 overall best weight: 0.7560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 431 HIS E 709 ASN ** E 758 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4742 r_free = 0.4742 target = 0.170944 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4574 r_free = 0.4574 target = 0.155724 restraints weight = 17543.565| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 46)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.157554 restraints weight = 13681.473| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 51)----------------| | r_work = 0.4617 r_free = 0.4617 target = 0.159148 restraints weight = 11141.157| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 44)----------------| | r_work = 0.4634 r_free = 0.4634 target = 0.160682 restraints weight = 9323.442| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 41)----------------| | r_work = 0.4647 r_free = 0.4647 target = 0.161844 restraints weight = 7878.810| |-----------------------------------------------------------------------------| r_work (final): 0.4656 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4472 moved from start: 1.0418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3378 Z= 0.116 Angle : 0.629 9.379 4580 Z= 0.316 Chirality : 0.042 0.132 549 Planarity : 0.005 0.038 578 Dihedral : 4.807 15.870 439 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 16.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -3.28 (0.41), residues: 405 helix: -2.61 (0.40), residues: 136 sheet: -1.98 (0.66), residues: 67 loop : -1.82 (0.45), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG E 496 TYR 0.010 0.001 TYR E 477 PHE 0.011 0.002 PHE E 611 TRP 0.028 0.003 TRP E 411 HIS 0.003 0.001 HIS E 431 Details of bonding type rmsd covalent geometry : bond 0.00261 ( 3378) covalent geometry : angle 0.62926 ( 4580) hydrogen bonds : bond 0.02745 ( 72) hydrogen bonds : angle 5.40461 ( 159) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 954.05 seconds wall clock time: 17 minutes 1.80 seconds (1021.80 seconds total)