Starting phenix.real_space_refine on Tue Feb 11 00:31:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7j_28905/02_2025/8f7j_28905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7j_28905/02_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_28905/02_2025/8f7j_28905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7j_28905/02_2025/8f7j_28905.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7j_28905/02_2025/8f7j_28905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7j_28905/02_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-5592/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: 3.79, per 1000 atoms: 1.14 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: 0.73 Conformation dependent library (CDL) restraints added in 368.4 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: 0.40 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: 0.85 Time building geometry restraints manager: 0.85 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: 3.120 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: 0.030 Set scattering table: 0.040 Process input model: 13.590 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.690 ------------------------------------------------------------------------------- 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= 0.336 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 *********************** 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 : 0.366 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: 0.1747 time to fit residues: 19.6519 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 : 0.355 ------------------------------------------------------------------------------- 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: 0.8980 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: 0.6986 ------------------------------------------------------------------------------- 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 = 0.188094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4792 r_free = 0.4792 target = 0.175938 restraints weight = 17622.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4812 r_free = 0.4812 target = 0.177472 restraints weight = 13970.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4831 r_free = 0.4831 target = 0.178859 restraints weight = 11504.676| |-----------------------------------------------------------------------------| r_work (final): 0.4803 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3695 moved from start: 0.4072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3378 Z= 0.204 Angle : 0.670 9.650 4580 Z= 0.340 Chirality : 0.046 0.154 549 Planarity : 0.006 0.046 578 Dihedral : 5.282 19.834 439 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % 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: -3.41 (0.38), residues: 405 helix: -2.78 (0.38), residues: 136 sheet: -1.97 (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 0.005 0.001 HIS E 522 PHE 0.013 0.002 PHE E 611 TYR 0.024 0.003 TYR E 477 ARG 0.004 0.001 ARG E 492 *********************** 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 : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 410 GLU cc_start: 0.7652 (tp30) cc_final: 0.7438 (tp30) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1381 time to fit residues: 10.1992 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 : 0.393 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 2.9990 chunk 36 optimal weight: 0.0040 chunk 16 optimal weight: 9.9990 chunk 1 optimal weight: 0.0370 chunk 34 optimal weight: 0.6980 chunk 38 optimal weight: 5.9990 chunk 32 optimal weight: 0.9990 chunk 6 optimal weight: 6.9990 chunk 30 optimal weight: 6.9990 chunk 25 optimal weight: 1.9990 overall best weight: 0.7474 ------------------------------------------------------------------------------- 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 = 0.4929 r_free = 0.4929 target = 0.187670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4774 r_free = 0.4774 target = 0.174728 restraints weight = 17357.717| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4799 r_free = 0.4799 target = 0.176603 restraints weight = 13460.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4817 r_free = 0.4817 target = 0.178072 restraints weight = 10761.811| |-----------------------------------------------------------------------------| r_work (final): 0.4782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3882 moved from start: 0.5348 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3378 Z= 0.168 Angle : 0.623 6.746 4580 Z= 0.310 Chirality : 0.044 0.197 549 Planarity : 0.004 0.032 578 Dihedral : 4.831 20.178 439 Min Nonbonded Distance : 2.580 Molprobity Statistics. All-atom Clashscore : 17.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 4.50 % Favored : 95.50 % 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: -3.31 (0.39), residues: 405 helix: -2.58 (0.40), residues: 135 sheet: -2.38 (0.77), residues: 45 loop : -1.88 (0.39), residues: 225 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 647 HIS 0.004 0.001 HIS E 431 PHE 0.013 0.002 PHE E 611 TYR 0.020 0.002 TYR E 477 ARG 0.003 0.000 ARG E 762 *********************** 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 : 0.374 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1431 time to fit residues: 9.2102 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 : 0.366 ------------------------------------------------------------------------------- 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: 8.9990 chunk 33 optimal weight: 4.9990 chunk 12 optimal weight: 9.9990 chunk 26 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 chunk 9 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 chunk 14 optimal weight: 10.0000 chunk 7 optimal weight: 0.9980 chunk 16 optimal weight: 9.9990 overall best weight: 1.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4881 r_free = 0.4881 target = 0.182498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.4712 r_free = 0.4712 target = 0.168912 restraints weight = 17290.797| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4736 r_free = 0.4736 target = 0.170637 restraints weight = 13493.058| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4758 r_free = 0.4758 target = 0.172398 restraints weight = 11041.819| |-----------------------------------------------------------------------------| r_work (final): 0.4726 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4225 moved from start: 0.6677 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3378 Z= 0.242 Angle : 0.706 5.685 4580 Z= 0.354 Chirality : 0.046 0.179 549 Planarity : 0.005 0.034 578 Dihedral : 5.117 18.631 439 Min Nonbonded Distance : 2.563 Molprobity Statistics. All-atom Clashscore : 19.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % Rotamer: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % 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: -3.48 (0.39), residues: 405 helix: -2.68 (0.38), residues: 136 sheet: -2.67 (0.78), residues: 50 loop : -1.92 (0.40), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP E 647 HIS 0.004 0.001 HIS E 608 PHE 0.011 0.002 PHE E 682 TYR 0.029 0.003 TYR E 513 ARG 0.008 0.001 ARG E 545 *********************** 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 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.339 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 440 ASP cc_start: 0.7853 (t0) cc_final: 0.7651 (t0) REVERT: E 471 LEU cc_start: 0.6614 (tp) cc_final: 0.6283 (tp) REVERT: E 475 TRP cc_start: 0.6213 (m-10) cc_final: 0.4630 (m-10) REVERT: E 477 TYR cc_start: 0.6497 (m-10) cc_final: 0.5454 (m-10) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1379 time to fit residues: 9.0681 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 : 0.396 ------------------------------------------------------------------------------- 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: 2.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 7.9990 chunk 5 optimal weight: 8.9990 chunk 8 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 30 optimal weight: 0.0170 chunk 4 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 25 optimal weight: 0.7980 overall best weight: 1.1420 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 649 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4874 r_free = 0.4874 target = 0.180745 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.4724 r_free = 0.4724 target = 0.168410 restraints weight = 17400.465| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4750 r_free = 0.4750 target = 0.170166 restraints weight = 13622.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4769 r_free = 0.4769 target = 0.171431 restraints weight = 10842.853| |-----------------------------------------------------------------------------| r_work (final): 0.4744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4224 moved from start: 0.7335 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= 0.179 Angle : 0.600 6.157 4580 Z= 0.303 Chirality : 0.043 0.142 549 Planarity : 0.004 0.033 578 Dihedral : 4.779 17.405 439 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.68 % Favored : 94.32 % Rotamer: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % 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: -3.31 (0.39), residues: 405 helix: -2.72 (0.37), residues: 135 sheet: -2.06 (0.75), residues: 56 loop : -1.80 (0.41), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP E 647 HIS 0.003 0.001 HIS E 568 PHE 0.010 0.002 PHE E 611 TYR 0.010 0.002 TYR E 477 ARG 0.003 0.000 ARG E 492 *********************** 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 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.375 Fit side-chains revert: symmetry clash REVERT: E 410 GLU cc_start: 0.6849 (tm-30) cc_final: 0.4930 (tm-30) REVERT: E 433 PHE cc_start: 0.5076 (t80) cc_final: 0.4730 (t80) REVERT: E 471 LEU cc_start: 0.6504 (tp) cc_final: 0.6201 (tp) REVERT: E 475 TRP cc_start: 0.5961 (m-10) cc_final: 0.4540 (m-10) REVERT: E 477 TYR cc_start: 0.6393 (m-10) cc_final: 0.5252 (m-10) REVERT: E 658 ILE cc_start: 0.5447 (tp) cc_final: 0.5050 (mm) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1262 time to fit residues: 8.0854 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 : 0.402 ------------------------------------------------------------------------------- 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: 0.5980 chunk 23 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.3980 chunk 24 optimal weight: 5.9990 chunk 5 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 12 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 672 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 = 0.4853 r_free = 0.4853 target = 0.179912 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.167309 restraints weight = 17727.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4735 r_free = 0.4735 target = 0.169127 restraints weight = 13792.847| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4754 r_free = 0.4754 target = 0.170727 restraints weight = 11000.190| |-----------------------------------------------------------------------------| r_work (final): 0.4727 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4267 moved from start: 0.7816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3378 Z= 0.150 Angle : 0.568 6.282 4580 Z= 0.286 Chirality : 0.042 0.186 549 Planarity : 0.004 0.029 578 Dihedral : 4.485 16.088 439 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 15.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.19 % Favored : 94.81 % Rotamer: Outliers : 0.00 % Allowed : 1.85 % Favored : 98.15 % 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: -3.09 (0.40), residues: 405 helix: -2.53 (0.40), residues: 135 sheet: -1.96 (0.74), residues: 56 loop : -1.67 (0.43), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.003 TRP E 411 HIS 0.003 0.001 HIS E 568 PHE 0.008 0.001 PHE E 699 TYR 0.007 0.001 TYR E 477 ARG 0.002 0.000 ARG E 492 *********************** 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 : 0.390 Fit side-chains revert: symmetry clash REVERT: E 471 LEU cc_start: 0.6572 (tp) cc_final: 0.6240 (tp) REVERT: E 475 TRP cc_start: 0.6155 (m-10) cc_final: 0.4773 (m-10) REVERT: E 477 TYR cc_start: 0.6394 (m-10) cc_final: 0.5301 (m-10) REVERT: E 498 LEU cc_start: 0.5284 (tp) cc_final: 0.5056 (tp) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1289 time to fit residues: 8.4582 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 : 0.377 ------------------------------------------------------------------------------- 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: 2.9990 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 7.9990 chunk 5 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 2.9990 chunk 19 optimal weight: 6.9990 chunk 34 optimal weight: 0.6980 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 494 ASN ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 695 ASN ** 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 = 0.4804 r_free = 0.4804 target = 0.174749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4651 r_free = 0.4651 target = 0.162735 restraints weight = 17359.830| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.164355 restraints weight = 13525.225| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4689 r_free = 0.4689 target = 0.165469 restraints weight = 10859.099| |-----------------------------------------------------------------------------| r_work (final): 0.4666 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4508 moved from start: 0.8833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3378 Z= 0.220 Angle : 0.662 6.199 4580 Z= 0.336 Chirality : 0.044 0.191 549 Planarity : 0.005 0.036 578 Dihedral : 5.050 15.986 439 Min Nonbonded Distance : 2.450 Molprobity Statistics. All-atom Clashscore : 19.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.65 % Favored : 92.35 % 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 (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 (0.41), residues: 405 helix: -2.73 (0.39), residues: 136 sheet: -2.42 (0.70), residues: 62 loop : -1.72 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 411 HIS 0.003 0.001 HIS E 499 PHE 0.014 0.003 PHE E 635 TYR 0.006 0.001 TYR E 668 ARG 0.005 0.001 ARG E 492 *********************** 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 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.390 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 475 TRP cc_start: 0.5889 (m-10) cc_final: 0.4929 (m-10) REVERT: E 477 TYR cc_start: 0.6393 (m-10) cc_final: 0.5629 (m-10) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1101 time to fit residues: 7.1820 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 : 0.302 ------------------------------------------------------------------------------- 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: 0.9980 chunk 19 optimal weight: 0.0770 chunk 39 optimal weight: 0.9980 chunk 8 optimal weight: 9.9990 chunk 10 optimal weight: 2.9990 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 5.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 chunk 37 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4811 r_free = 0.4811 target = 0.175603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4670 r_free = 0.4670 target = 0.164366 restraints weight = 17136.588| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4686 r_free = 0.4686 target = 0.165536 restraints weight = 13598.497| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4702 r_free = 0.4702 target = 0.166666 restraints weight = 11090.506| |-----------------------------------------------------------------------------| r_work (final): 0.4698 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4315 moved from start: 0.9073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3378 Z= 0.159 Angle : 0.604 10.080 4580 Z= 0.304 Chirality : 0.042 0.131 549 Planarity : 0.004 0.036 578 Dihedral : 4.560 14.416 439 Min Nonbonded Distance : 2.376 Molprobity Statistics. All-atom Clashscore : 14.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % 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 (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: -3.13 (0.41), residues: 405 helix: -2.57 (0.40), residues: 135 sheet: -1.53 (0.71), residues: 63 loop : -1.82 (0.45), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 647 HIS 0.003 0.000 HIS E 568 PHE 0.010 0.002 PHE E 611 TYR 0.005 0.001 TYR E 513 ARG 0.002 0.000 ARG E 492 *********************** 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 46 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.377 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 521 LEU cc_start: 0.5632 (mt) cc_final: 0.5398 (mt) REVERT: E 658 ILE cc_start: 0.5121 (tp) cc_final: 0.4707 (mm) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1260 time to fit residues: 7.7714 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 : 0.300 ------------------------------------------------------------------------------- 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: 8.9990 chunk 39 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 19 optimal weight: 0.4980 chunk 37 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 25 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4802 r_free = 0.4802 target = 0.174869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.4655 r_free = 0.4655 target = 0.163169 restraints weight = 17328.469| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4673 r_free = 0.4673 target = 0.164476 restraints weight = 13490.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.165894 restraints weight = 11044.549| |-----------------------------------------------------------------------------| r_work (final): 0.4693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4295 moved from start: 0.9383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3378 Z= 0.156 Angle : 0.585 6.963 4580 Z= 0.295 Chirality : 0.041 0.132 549 Planarity : 0.004 0.035 578 Dihedral : 4.401 13.596 439 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 14.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % 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 (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: -3.19 (0.41), residues: 405 helix: -2.52 (0.40), residues: 135 sheet: -2.45 (0.65), residues: 70 loop : -1.54 (0.45), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.003 TRP E 411 HIS 0.003 0.000 HIS E 568 PHE 0.010 0.001 PHE E 611 TYR 0.004 0.001 TYR E 513 ARG 0.002 0.000 ARG E 492 *********************** 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 47 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 47 time to evaluate : 0.376 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 498 LEU cc_start: 0.5241 (tp) cc_final: 0.5039 (tp) REVERT: E 521 LEU cc_start: 0.5503 (mt) cc_final: 0.5280 (mt) REVERT: E 658 ILE cc_start: 0.5015 (tp) cc_final: 0.4589 (mm) outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1164 time to fit residues: 7.6036 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 : 0.432 ------------------------------------------------------------------------------- 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: 0.4980 chunk 38 optimal weight: 5.9990 chunk 10 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 29 optimal weight: 0.1980 chunk 30 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 4.9990 chunk 18 optimal weight: 5.9990 overall best weight: 1.4582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 HIS ** E 672 ASN ** 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 = 0.4755 r_free = 0.4755 target = 0.170782 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 70)----------------| | r_work = 0.4605 r_free = 0.4605 target = 0.158202 restraints weight = 17320.803| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 56)----------------| | r_work = 0.4628 r_free = 0.4628 target = 0.159912 restraints weight = 13347.168| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4646 r_free = 0.4646 target = 0.161387 restraints weight = 10748.005| |-----------------------------------------------------------------------------| r_work (final): 0.4647 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4536 moved from start: 1.0217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 3378 Z= 0.207 Angle : 0.659 6.369 4580 Z= 0.334 Chirality : 0.044 0.133 549 Planarity : 0.005 0.043 578 Dihedral : 4.920 16.478 439 Min Nonbonded Distance : 2.375 Molprobity Statistics. All-atom Clashscore : 19.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.40 % Favored : 91.60 % 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: -3.14 (0.42), residues: 405 helix: -2.81 (0.38), residues: 135 sheet: -2.02 (0.63), residues: 81 loop : -1.35 (0.47), residues: 189 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP E 411 HIS 0.003 0.001 HIS E 568 PHE 0.014 0.002 PHE E 611 TYR 0.009 0.001 TYR E 668 ARG 0.005 0.001 ARG E 403 ********************** 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 46 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 46 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 498 LEU cc_start: 0.5564 (tp) cc_final: 0.5257 (tp) REVERT: E 521 LEU cc_start: 0.5518 (mt) cc_final: 0.5183 (mt) REVERT: E 704 ILE cc_start: 0.5401 (tp) cc_final: 0.5101 (tp) outliers start: 0 outliers final: 0 residues processed: 46 average time/residue: 0.1014 time to fit residues: 6.5947 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 : 0.365 ------------------------------------------------------------------------------- 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: 10.0000 chunk 5 optimal weight: 0.0770 chunk 16 optimal weight: 0.4980 chunk 36 optimal weight: 0.4980 chunk 20 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 4.9990 chunk 2 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 39 optimal weight: 0.0060 chunk 24 optimal weight: 1.9990 overall best weight: 0.3954 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 576 ASN ** E 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4785 r_free = 0.4785 target = 0.172731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.4633 r_free = 0.4633 target = 0.160323 restraints weight = 17142.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 47)----------------| | r_work = 0.4659 r_free = 0.4659 target = 0.162175 restraints weight = 13230.400| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.4678 r_free = 0.4678 target = 0.163529 restraints weight = 10496.340| |-----------------------------------------------------------------------------| r_work (final): 0.4676 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4378 moved from start: 1.0279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 3378 Z= 0.165 Angle : 0.591 6.572 4580 Z= 0.298 Chirality : 0.042 0.144 549 Planarity : 0.005 0.066 578 Dihedral : 4.456 15.063 439 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % 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: -3.05 (0.42), residues: 405 helix: -2.68 (0.39), residues: 135 sheet: -1.92 (0.65), residues: 80 loop : -1.37 (0.46), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP E 411 HIS 0.003 0.001 HIS E 568 PHE 0.008 0.001 PHE E 611 TYR 0.007 0.001 TYR E 477 ARG 0.002 0.000 ARG E 731 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1714.29 seconds wall clock time: 31 minutes 15.01 seconds (1875.01 seconds total)