Starting phenix.real_space_refine on Fri Dec 27 07:34:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7j_28905/12_2024/8f7j_28905.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7j_28905/12_2024/8f7j_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_28905/12_2024/8f7j_28905.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7j_28905/12_2024/8f7j_28905.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7j_28905/12_2024/8f7j_28905.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7j_28905/12_2024/8f7j_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-5532/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: 3.69, per 1000 atoms: 1.11 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: 0.80 Conformation dependent library (CDL) restraints added in 459.7 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: 0.83 Time building geometry restraints manager: 0.95 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: 3.200 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 13.990 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.210 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.670 ------------------------------------------------------------------------------- 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 : 0.433 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: 0.1978 time to fit residues: 22.2042 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 : 0.423 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3643 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 : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 ASN cc_start: 0.8651 (m-40) cc_final: 0.8319 (m110) REVERT: E 410 GLU cc_start: 0.8621 (tp30) cc_final: 0.8187 (tp30) REVERT: E 434 MET cc_start: 0.7479 (tmm) cc_final: 0.7260 (tmm) REVERT: E 448 LEU cc_start: 0.8020 (tp) cc_final: 0.7792 (tp) outliers start: 0 outliers final: 0 residues processed: 59 average time/residue: 0.1670 time to fit residues: 12.3850 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 : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 36 optimal weight: 0.0040 chunk 39 optimal weight: 9.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 5.9990 chunk 27 optimal weight: 5.9990 chunk 18 optimal weight: 0.0010 overall best weight: 0.7402 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.3762 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.058 3378 Z= 0.175 Angle : 0.613 6.767 4580 Z= 0.308 Chirality : 0.044 0.188 549 Planarity : 0.004 0.031 578 Dihedral : 4.827 19.776 439 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 17.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.30 (0.39), residues: 405 helix: -2.56 (0.40), residues: 135 sheet: -2.28 (0.78), residues: 45 loop : -1.90 (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 0.012 0.002 PHE E 611 TYR 0.020 0.002 TYR E 477 ARG 0.003 0.000 ARG E 419 *********************** 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 51 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.396 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 ASN cc_start: 0.8724 (m-40) cc_final: 0.8388 (m110) REVERT: E 448 LEU cc_start: 0.7873 (tp) cc_final: 0.7631 (tp) REVERT: E 647 TRP cc_start: 0.6954 (p90) cc_final: 0.6476 (p90) outliers start: 0 outliers final: 0 residues processed: 51 average time/residue: 0.1440 time to fit residues: 9.4523 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 : 0.404 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.0040 chunk 38 optimal weight: 7.9990 chunk 19 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 10 optimal weight: 8.9990 chunk 32 optimal weight: 0.4980 chunk 21 optimal weight: 8.9990 chunk 0 optimal weight: 5.9990 overall best weight: 1.8796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 560 GLN ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 608 HIS E 649 ASN E 711 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4216 moved from start: 0.7079 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= 0.259 Angle : 0.763 6.140 4580 Z= 0.379 Chirality : 0.047 0.184 549 Planarity : 0.005 0.041 578 Dihedral : 5.464 18.841 439 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 20.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 4.76 % Favored : 95.24 % 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: -3.56 (0.39), residues: 405 helix: -2.81 (0.36), residues: 135 sheet: -2.69 (0.76), residues: 51 loop : -1.93 (0.41), residues: 219 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.004 TRP E 647 HIS 0.004 0.001 HIS E 608 PHE 0.014 0.002 PHE E 728 TYR 0.014 0.002 TYR E 477 ARG 0.007 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 55 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.419 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 ASN cc_start: 0.8870 (m-40) cc_final: 0.8577 (m110) REVERT: E 410 GLU cc_start: 0.8831 (tp30) cc_final: 0.8444 (tp30) REVERT: E 411 TRP cc_start: 0.5977 (m100) cc_final: 0.5567 (m100) REVERT: E 440 ASP cc_start: 0.8359 (t0) cc_final: 0.8056 (t0) REVERT: E 471 LEU cc_start: 0.6943 (tp) cc_final: 0.6686 (tp) REVERT: E 475 TRP cc_start: 0.7286 (m-10) cc_final: 0.5674 (m-10) REVERT: E 477 TYR cc_start: 0.7668 (m-10) cc_final: 0.5984 (m-10) REVERT: E 491 LEU cc_start: 0.8712 (mt) cc_final: 0.8440 (mm) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1318 time to fit residues: 9.4338 Evaluate side-chains 43 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 43 time to evaluate : 0.481 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 5.9990 chunk 15 optimal weight: 0.9990 chunk 32 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 9 optimal weight: 10.0000 chunk 13 optimal weight: 8.9990 chunk 7 optimal weight: 1.9990 chunk 22 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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** ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4190 moved from start: 0.7637 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= 0.183 Angle : 0.590 6.307 4580 Z= 0.303 Chirality : 0.043 0.142 549 Planarity : 0.004 0.033 578 Dihedral : 4.770 17.081 439 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % 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: -3.49 (0.39), residues: 405 helix: -2.81 (0.37), residues: 135 sheet: -2.53 (0.78), residues: 50 loop : -1.88 (0.41), residues: 220 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 647 HIS 0.003 0.001 HIS E 737 PHE 0.010 0.001 PHE E 611 TYR 0.025 0.002 TYR E 513 ARG 0.004 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 54 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.414 Fit side-chains revert: symmetry clash REVERT: E 406 ASN cc_start: 0.8896 (m-40) cc_final: 0.8600 (m110) REVERT: E 410 GLU cc_start: 0.8830 (tp30) cc_final: 0.8383 (tp30) REVERT: E 411 TRP cc_start: 0.5896 (m100) cc_final: 0.5582 (m100) REVERT: E 440 ASP cc_start: 0.8366 (t0) cc_final: 0.8097 (t0) REVERT: E 471 LEU cc_start: 0.6861 (tp) cc_final: 0.6637 (tp) REVERT: E 475 TRP cc_start: 0.7164 (m-10) cc_final: 0.5592 (m-10) REVERT: E 477 TYR cc_start: 0.7649 (m-10) cc_final: 0.6280 (m-10) REVERT: E 498 LEU cc_start: 0.6897 (tt) cc_final: 0.6690 (tp) REVERT: E 658 ILE cc_start: 0.5608 (tp) cc_final: 0.5197 (mm) REVERT: E 696 ASN cc_start: 0.6517 (t0) cc_final: 0.6264 (t0) outliers start: 0 outliers final: 0 residues processed: 54 average time/residue: 0.1375 time to fit residues: 9.6092 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 : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 0.8980 chunk 38 optimal weight: 7.9990 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 7.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.0370 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 4 optimal weight: 0.0770 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9990 overall best weight: 0.5418 ------------------------------------------------------------------------------- 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 718 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4152 moved from start: 0.7957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3378 Z= 0.168 Angle : 0.573 6.354 4580 Z= 0.290 Chirality : 0.042 0.162 549 Planarity : 0.004 0.035 578 Dihedral : 4.532 16.204 439 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 14.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.42 % Favored : 93.58 % 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: -3.31 (0.41), residues: 405 helix: -2.66 (0.39), residues: 136 sheet: -2.08 (0.67), residues: 68 loop : -1.78 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP E 647 HIS 0.003 0.000 HIS E 568 PHE 0.009 0.001 PHE E 611 TYR 0.029 0.002 TYR E 513 ARG 0.002 0.000 ARG E 419 *********************** 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 53 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.431 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 ASN cc_start: 0.8864 (m-40) cc_final: 0.8595 (m110) REVERT: E 410 GLU cc_start: 0.8853 (tp30) cc_final: 0.8051 (tp30) REVERT: E 411 TRP cc_start: 0.5946 (m100) cc_final: 0.5523 (m100) REVERT: E 433 PHE cc_start: 0.6448 (t80) cc_final: 0.5829 (t80) REVERT: E 440 ASP cc_start: 0.8342 (t0) cc_final: 0.8033 (t0) REVERT: E 475 TRP cc_start: 0.6969 (m-10) cc_final: 0.6341 (m-10) REVERT: E 658 ILE cc_start: 0.5529 (tp) cc_final: 0.5146 (mm) outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.1262 time to fit residues: 9.0167 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 : 0.377 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 0.7980 chunk 17 optimal weight: 8.9990 chunk 15 optimal weight: 0.0770 chunk 11 optimal weight: 6.9990 chunk 7 optimal weight: 6.9990 chunk 26 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.5342 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4407 moved from start: 0.9148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3378 Z= 0.219 Angle : 0.676 5.975 4580 Z= 0.343 Chirality : 0.044 0.125 549 Planarity : 0.005 0.041 578 Dihedral : 5.169 16.176 439 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 18.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.14 % Favored : 90.86 % Rotamer: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.40 (0.41), residues: 405 helix: -2.82 (0.38), residues: 136 sheet: -1.82 (0.69), residues: 68 loop : -1.90 (0.44), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 647 HIS 0.004 0.001 HIS E 499 PHE 0.018 0.003 PHE E 728 TYR 0.023 0.002 TYR E 513 ARG 0.004 0.001 ARG E 688 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 810 Ramachandran restraints generated. 405 Oldfield, 0 Emsley, 405 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 406 ASN cc_start: 0.8894 (m-40) cc_final: 0.8657 (m110) REVERT: E 440 ASP cc_start: 0.8313 (t0) cc_final: 0.8031 (t0) REVERT: E 696 ASN cc_start: 0.6660 (t0) cc_final: 0.6437 (t0) REVERT: E 758 GLN cc_start: 0.5707 (tp-100) cc_final: 0.5496 (tp-100) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1096 time to fit residues: 7.8396 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 : 0.608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 0.8980 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.0020 chunk 33 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 15 optimal weight: 2.9990 chunk 28 optimal weight: 3.9990 chunk 11 optimal weight: 7.9990 chunk 32 optimal weight: 0.8980 chunk 23 optimal weight: 4.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 499 HIS ** E 575 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 695 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4327 moved from start: 0.9322 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= 0.157 Angle : 0.561 6.353 4580 Z= 0.287 Chirality : 0.042 0.159 549 Planarity : 0.004 0.034 578 Dihedral : 4.620 14.708 439 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 15.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.00 % Allowed : 1.32 % Favored : 98.68 % 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: -3.20 (0.41), residues: 405 helix: -2.60 (0.40), residues: 135 sheet: -1.45 (0.71), residues: 63 loop : -1.93 (0.44), residues: 207 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 647 HIS 0.003 0.001 HIS E 568 PHE 0.010 0.001 PHE E 611 TYR 0.023 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 50 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 50 time to evaluate : 0.475 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 ASN cc_start: 0.8902 (m-40) cc_final: 0.8661 (m110) REVERT: E 440 ASP cc_start: 0.8493 (t0) cc_final: 0.8168 (t0) REVERT: E 475 TRP cc_start: 0.6955 (m-10) cc_final: 0.6745 (m100) outliers start: 0 outliers final: 0 residues processed: 50 average time/residue: 0.1215 time to fit residues: 8.1633 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 : 0.413 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 2.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 5.9990 chunk 26 optimal weight: 0.5980 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 chunk 3 optimal weight: 3.9990 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 10.0000 chunk 25 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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 758 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4366 moved from start: 0.9728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 3378 Z= 0.159 Angle : 0.561 6.434 4580 Z= 0.285 Chirality : 0.042 0.148 549 Planarity : 0.004 0.035 578 Dihedral : 4.569 14.612 439 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 15.85 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: -3.38 (0.40), residues: 405 helix: -2.71 (0.39), residues: 143 sheet: -2.11 (0.62), residues: 80 loop : -1.71 (0.45), residues: 182 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 647 HIS 0.002 0.000 HIS E 568 PHE 0.010 0.001 PHE E 611 TYR 0.021 0.002 TYR E 513 ARG 0.003 0.000 ARG E 765 *********************** 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 52 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 52 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 406 ASN cc_start: 0.8905 (m-40) cc_final: 0.8673 (m110) REVERT: E 440 ASP cc_start: 0.8504 (t0) cc_final: 0.8173 (t0) REVERT: E 453 LEU cc_start: 0.8035 (tt) cc_final: 0.7736 (tt) REVERT: E 658 ILE cc_start: 0.5558 (tp) cc_final: 0.5110 (mm) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.1202 time to fit residues: 8.3788 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 : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 13 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4445 moved from start: 1.0173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3378 Z= 0.183 Angle : 0.625 9.552 4580 Z= 0.313 Chirality : 0.042 0.145 549 Planarity : 0.005 0.036 578 Dihedral : 4.757 15.896 439 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 18.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.64 % Favored : 91.36 % 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: -3.35 (0.41), residues: 405 helix: -2.72 (0.38), residues: 144 sheet: -1.96 (0.64), residues: 80 loop : -1.72 (0.45), residues: 181 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP E 647 HIS 0.009 0.002 HIS E 499 PHE 0.012 0.002 PHE E 611 TYR 0.021 0.002 TYR E 513 ARG 0.004 0.001 ARG E 492 ********************** 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 49 residues out of total 378 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 49 time to evaluate : 0.367 Fit side-chains REVERT: E 406 ASN cc_start: 0.8905 (m-40) cc_final: 0.8684 (m110) REVERT: E 440 ASP cc_start: 0.8455 (t0) cc_final: 0.8145 (t0) REVERT: E 647 TRP cc_start: 0.7507 (p90) cc_final: 0.7056 (p90) REVERT: E 704 ILE cc_start: 0.5813 (tp) cc_final: 0.5612 (tp) outliers start: 0 outliers final: 0 residues processed: 49 average time/residue: 0.1120 time to fit residues: 7.6714 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 : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 7.9990 chunk 36 optimal weight: 0.0970 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 6.9990 chunk 1 optimal weight: 4.9990 chunk 25 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 23 optimal weight: 5.9990 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 6.9990 chunk 39 optimal weight: 6.9990 overall best weight: 2.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 660 ASN E 740 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 = 0.4682 r_free = 0.4682 target = 0.165522 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.151871 restraints weight = 17446.365| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.4533 r_free = 0.4533 target = 0.153473 restraints weight = 13572.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4550 r_free = 0.4550 target = 0.154801 restraints weight = 11043.750| |-----------------------------------------------------------------------------| r_work (final): 0.4545 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.4865 moved from start: 1.1574 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 3378 Z= 0.323 Angle : 0.823 8.254 4580 Z= 0.420 Chirality : 0.050 0.194 549 Planarity : 0.007 0.083 578 Dihedral : 6.027 20.668 439 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 27.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.36 % Favored : 88.64 % 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: -3.32 (0.41), residues: 405 helix: -2.95 (0.37), residues: 135 sheet: -1.69 (0.65), residues: 76 loop : -1.71 (0.47), residues: 194 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP E 475 HIS 0.012 0.003 HIS E 499 PHE 0.021 0.003 PHE E 611 TYR 0.021 0.003 TYR E 513 ARG 0.007 0.001 ARG E 492 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1382.75 seconds wall clock time: 26 minutes 53.26 seconds (1613.26 seconds total)