Starting phenix.real_space_refine on Fri Dec 27 15:26:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3j_15830/12_2024/8b3j_15830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3j_15830/12_2024/8b3j_15830.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8b3j_15830/12_2024/8b3j_15830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3j_15830/12_2024/8b3j_15830.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3j_15830/12_2024/8b3j_15830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3j_15830/12_2024/8b3j_15830.cif" } resolution = 3.1 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= 0.032 sd= 0.161 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 20 5.16 5 C 3635 2.51 5 N 976 2.21 5 O 1057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 11 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 5688 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2034 Number of conformers: 1 Conformer: "" Number of residues, atoms: 257, 2034 Classifications: {'peptide': 257} Link IDs: {'PTRANS': 24, 'TRANS': 232} Chain: "B" Number of atoms: 1456 Number of conformers: 1 Conformer: "" Number of residues, atoms: 183, 1456 Classifications: {'peptide': 183} Link IDs: {'PTRANS': 12, 'TRANS': 170} Chain breaks: 1 Chain: "C" Number of atoms: 2198 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 2198 Classifications: {'peptide': 278} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 262} Time building chain proxies: 4.01, per 1000 atoms: 0.70 Number of scatterers: 5688 At special positions: 0 Unit cell: (108.9, 101.2, 93.5, 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 20 16.00 O 1057 8.00 N 976 7.00 C 3635 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: 1.31 Conformation dependent library (CDL) restraints added in 669.9 milliseconds 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1326 Finding SS restraints... Secondary structure from input PDB file: 10 helices and 11 sheets defined 9.1% alpha, 29.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 665 through 670 Processing helix chain 'A' and resid 683 through 687 removed outlier: 3.750A pdb=" N THR A 686 " --> pdb=" O THR A 683 " (cutoff:3.500A) Processing helix chain 'A' and resid 731 through 736 Processing helix chain 'A' and resid 796 through 802 removed outlier: 3.636A pdb=" N GLN A 802 " --> pdb=" O THR A 798 " (cutoff:3.500A) Processing helix chain 'A' and resid 841 through 846 Processing helix chain 'B' and resid 112 through 119 Processing helix chain 'B' and resid 173 through 182 removed outlier: 3.678A pdb=" N THR B 179 " --> pdb=" O GLY B 175 " (cutoff:3.500A) removed outlier: 3.689A pdb=" N MET B 180 " --> pdb=" O HIS B 176 " (cutoff:3.500A) Processing helix chain 'C' and resid 375 through 379 Processing helix chain 'C' and resid 388 through 392 Processing helix chain 'C' and resid 441 through 447 removed outlier: 3.520A pdb=" N ALA C 446 " --> pdb=" O PRO C 442 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N THR C 447 " --> pdb=" O VAL C 443 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 640 through 641 removed outlier: 4.295A pdb=" N ASP C 400 " --> pdb=" O TRP C 580 " (cutoff:3.500A) removed outlier: 6.838A pdb=" N VAL C 582 " --> pdb=" O TYR C 398 " (cutoff:3.500A) removed outlier: 5.923A pdb=" N TYR C 398 " --> pdb=" O VAL C 582 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 674 through 678 removed outlier: 5.085A pdb=" N ALA A 870 " --> pdb=" O TYR A 676 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N ALA A 678 " --> pdb=" O TRP A 868 " (cutoff:3.500A) removed outlier: 6.261A pdb=" N TRP A 868 " --> pdb=" O ALA A 678 " (cutoff:3.500A) removed outlier: 3.562A pdb=" N PHE A 753 " --> pdb=" O ALA A 867 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ARG A 747 " --> pdb=" O ALA A 873 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N ASP C 361 " --> pdb=" O GLU A 823 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 783 through 788 removed outlier: 4.470A pdb=" N ARG A 849 " --> pdb=" O VAL A 772 " (cutoff:3.500A) removed outlier: 3.805A pdb=" N VAL A 772 " --> pdb=" O ARG A 849 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N LEU A 766 " --> pdb=" O LEU A 855 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 742 through 743 Processing sheet with id=AA5, first strand: chain 'A' and resid 890 through 891 Processing sheet with id=AA6, first strand: chain 'B' and resid 94 through 101 removed outlier: 5.474A pdb=" N ARG B 95 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 252 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET B 97 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 247 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL B 257 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG B 134 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU B 259 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR B 132 " --> pdb=" O LEU B 259 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLY B 197 " --> pdb=" O VAL B 141 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 94 through 101 removed outlier: 5.474A pdb=" N ARG B 95 " --> pdb=" O ALA B 252 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N ALA B 252 " --> pdb=" O ARG B 95 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N MET B 97 " --> pdb=" O VAL B 250 " (cutoff:3.500A) removed outlier: 3.677A pdb=" N THR B 247 " --> pdb=" O ASN B 144 " (cutoff:3.500A) removed outlier: 4.463A pdb=" N VAL B 257 " --> pdb=" O ARG B 134 " (cutoff:3.500A) removed outlier: 6.945A pdb=" N ARG B 134 " --> pdb=" O VAL B 257 " (cutoff:3.500A) removed outlier: 4.718A pdb=" N LEU B 259 " --> pdb=" O TYR B 132 " (cutoff:3.500A) removed outlier: 7.051A pdb=" N TYR B 132 " --> pdb=" O LEU B 259 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 108 through 111 removed outlier: 6.407A pdb=" N LYS B 152 " --> pdb=" O LEU B 230 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ALA B 232 " --> pdb=" O TYR B 150 " (cutoff:3.500A) removed outlier: 6.436A pdb=" N TYR B 150 " --> pdb=" O ALA B 232 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 494 through 498 removed outlier: 6.761A pdb=" N ARG C 470 " --> pdb=" O ASP C 564 " (cutoff:3.500A) removed outlier: 6.083A pdb=" N ASP C 564 " --> pdb=" O ARG C 470 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N ARG C 472 " --> pdb=" O VAL C 562 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N PHE C 415 " --> pdb=" O VAL C 559 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL C 561 " --> pdb=" O LEU C 413 " (cutoff:3.500A) removed outlier: 7.233A pdb=" N LEU C 413 " --> pdb=" O VAL C 561 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'C' and resid 427 through 428 removed outlier: 3.613A pdb=" N GLY C 437 " --> pdb=" O PHE C 427 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 518 through 519 149 hydrogen bonds defined for protein. 381 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.63 Time building geometry restraints manager: 1.55 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1864 1.34 - 1.46: 1073 1.46 - 1.57: 2880 1.57 - 1.69: 1 1.69 - 1.80: 34 Bond restraints: 5852 Sorted by residual: bond pdb=" CA GLU A 653 " pdb=" CB GLU A 653 " ideal model delta sigma weight residual 1.528 1.574 -0.046 2.61e-02 1.47e+03 3.05e+00 bond pdb=" CG1 ILE A 697 " pdb=" CD1 ILE A 697 " ideal model delta sigma weight residual 1.513 1.464 0.049 3.90e-02 6.57e+02 1.59e+00 bond pdb=" C LEU A 669 " pdb=" N VAL A 670 " ideal model delta sigma weight residual 1.338 1.328 0.010 1.01e-02 9.80e+03 9.95e-01 bond pdb=" CB GLU A 653 " pdb=" CG GLU A 653 " ideal model delta sigma weight residual 1.520 1.548 -0.028 3.00e-02 1.11e+03 8.88e-01 bond pdb=" CB ASP A 703 " pdb=" CG ASP A 703 " ideal model delta sigma weight residual 1.516 1.495 0.021 2.50e-02 1.60e+03 7.23e-01 ... (remaining 5847 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.32: 7612 1.32 - 2.64: 283 2.64 - 3.96: 64 3.96 - 5.28: 12 5.28 - 6.60: 3 Bond angle restraints: 7974 Sorted by residual: angle pdb=" N SER C 592 " pdb=" CA SER C 592 " pdb=" C SER C 592 " ideal model delta sigma weight residual 110.24 114.72 -4.48 1.30e+00 5.92e-01 1.19e+01 angle pdb=" C ALA C 591 " pdb=" N SER C 592 " pdb=" CA SER C 592 " ideal model delta sigma weight residual 120.82 125.31 -4.49 1.47e+00 4.63e-01 9.33e+00 angle pdb=" CA GLU A 653 " pdb=" CB GLU A 653 " pdb=" CG GLU A 653 " ideal model delta sigma weight residual 114.10 119.16 -5.06 2.00e+00 2.50e-01 6.40e+00 angle pdb=" CA PRO A 820 " pdb=" C PRO A 820 " pdb=" O PRO A 820 " ideal model delta sigma weight residual 121.38 119.45 1.93 7.70e-01 1.69e+00 6.28e+00 angle pdb=" N LEU B 230 " pdb=" CA LEU B 230 " pdb=" C LEU B 230 " ideal model delta sigma weight residual 113.12 110.18 2.94 1.25e+00 6.40e-01 5.54e+00 ... (remaining 7969 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.50: 2980 17.50 - 35.00: 359 35.00 - 52.51: 83 52.51 - 70.01: 12 70.01 - 87.51: 3 Dihedral angle restraints: 3437 sinusoidal: 1367 harmonic: 2070 Sorted by residual: dihedral pdb=" CA LEU A 880 " pdb=" C LEU A 880 " pdb=" N SER A 881 " pdb=" CA SER A 881 " ideal model delta harmonic sigma weight residual 180.00 -157.71 -22.29 0 5.00e+00 4.00e-02 1.99e+01 dihedral pdb=" CA SER B 213 " pdb=" C SER B 213 " pdb=" N GLU B 214 " pdb=" CA GLU B 214 " ideal model delta harmonic sigma weight residual 180.00 159.55 20.45 0 5.00e+00 4.00e-02 1.67e+01 dihedral pdb=" CA LEU A 832 " pdb=" C LEU A 832 " pdb=" N ARG A 833 " pdb=" CA ARG A 833 " ideal model delta harmonic sigma weight residual -180.00 -159.58 -20.42 0 5.00e+00 4.00e-02 1.67e+01 ... (remaining 3434 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 582 0.041 - 0.081: 191 0.081 - 0.121: 77 0.121 - 0.162: 5 0.162 - 0.202: 1 Chirality restraints: 856 Sorted by residual: chirality pdb=" CA ILE A 697 " pdb=" N ILE A 697 " pdb=" C ILE A 697 " pdb=" CB ILE A 697 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.02e+00 chirality pdb=" CA ILE B 248 " pdb=" N ILE B 248 " pdb=" C ILE B 248 " pdb=" CB ILE B 248 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.91e-01 chirality pdb=" CA ILE C 475 " pdb=" N ILE C 475 " pdb=" C ILE C 475 " pdb=" CB ILE C 475 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.67e-01 ... (remaining 853 not shown) Planarity restraints: 1048 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 714 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.29e+00 pdb=" N PRO A 715 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO A 715 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 715 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR B 158 " -0.024 5.00e-02 4.00e+02 3.61e-02 2.09e+00 pdb=" N PRO B 159 " 0.062 5.00e-02 4.00e+02 pdb=" CA PRO B 159 " -0.019 5.00e-02 4.00e+02 pdb=" CD PRO B 159 " -0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL A 775 " -0.020 5.00e-02 4.00e+02 2.99e-02 1.43e+00 pdb=" N PRO A 776 " 0.052 5.00e-02 4.00e+02 pdb=" CA PRO A 776 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 776 " -0.017 5.00e-02 4.00e+02 ... (remaining 1045 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.70: 195 2.70 - 3.25: 5010 3.25 - 3.80: 7952 3.80 - 4.35: 10703 4.35 - 4.90: 18898 Nonbonded interactions: 42758 Sorted by model distance: nonbonded pdb=" O GLY B 145 " pdb=" OG SER B 194 " model vdw 2.144 3.040 nonbonded pdb=" OE1 GLU B 131 " pdb=" OG SER B 213 " model vdw 2.162 3.040 nonbonded pdb=" ND2 ASN A 796 " pdb=" OE1 GLU A 799 " model vdw 2.192 3.120 nonbonded pdb=" OG SER C 364 " pdb=" O THR C 366 " model vdw 2.216 3.040 nonbonded pdb=" N GLU A 653 " pdb=" OE1 GLU A 653 " model vdw 2.222 3.120 ... (remaining 42753 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.780 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 16.780 Find NCS groups from input model: 0.070 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:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 0.049 5852 Z= 0.313 Angle : 0.630 6.597 7974 Z= 0.337 Chirality : 0.046 0.202 856 Planarity : 0.004 0.038 1048 Dihedral : 15.709 87.512 2111 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 7.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 0.00 % Allowed : 19.09 % Favored : 80.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.49 (0.30), residues: 710 helix: -2.08 (0.67), residues: 54 sheet: -0.62 (0.37), residues: 194 loop : -2.19 (0.27), residues: 462 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 453 HIS 0.004 0.001 HIS A 731 PHE 0.015 0.002 PHE C 402 TYR 0.013 0.001 TYR A 663 ARG 0.003 0.000 ARG A 698 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.699 Fit side-chains REVERT: A 812 TYR cc_start: 0.8801 (t80) cc_final: 0.8053 (t80) outliers start: 0 outliers final: 0 residues processed: 72 average time/residue: 0.2308 time to fit residues: 21.1041 Evaluate side-chains 68 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.679 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 59 optimal weight: 20.0000 chunk 53 optimal weight: 8.9990 chunk 29 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 35 optimal weight: 9.9990 chunk 28 optimal weight: 5.9990 chunk 54 optimal weight: 0.6980 chunk 21 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 63 optimal weight: 6.9990 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 543 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8601 moved from start: 0.0655 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5852 Z= 0.259 Angle : 0.592 6.817 7974 Z= 0.312 Chirality : 0.046 0.177 856 Planarity : 0.005 0.057 1048 Dihedral : 4.664 21.740 786 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 2.59 % Allowed : 18.45 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.46 (0.30), residues: 710 helix: -2.19 (0.59), residues: 65 sheet: -0.62 (0.36), residues: 204 loop : -2.14 (0.27), residues: 441 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 453 HIS 0.005 0.001 HIS A 731 PHE 0.010 0.001 PHE C 427 TYR 0.012 0.001 TYR B 150 ARG 0.001 0.000 ARG C 460 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 72 time to evaluate : 0.773 Fit side-chains REVERT: A 812 TYR cc_start: 0.8795 (t80) cc_final: 0.8091 (t80) REVERT: B 234 LYS cc_start: 0.8501 (mttm) cc_final: 0.8015 (mmtm) outliers start: 16 outliers final: 10 residues processed: 86 average time/residue: 0.2215 time to fit residues: 24.4958 Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 69 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 35 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 52 optimal weight: 10.0000 chunk 43 optimal weight: 9.9990 chunk 17 optimal weight: 20.0000 chunk 63 optimal weight: 10.0000 chunk 68 optimal weight: 0.8980 chunk 56 optimal weight: 20.0000 chunk 21 optimal weight: 20.0000 chunk 51 optimal weight: 30.0000 chunk 62 optimal weight: 8.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- 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: 0.8627 moved from start: 0.0823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.045 5852 Z= 0.370 Angle : 0.634 7.172 7974 Z= 0.334 Chirality : 0.048 0.176 856 Planarity : 0.005 0.051 1048 Dihedral : 4.907 22.915 786 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.03 % Favored : 91.97 % Rotamer: Outliers : 4.37 % Allowed : 18.28 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.50 (0.30), residues: 710 helix: -2.44 (0.56), residues: 66 sheet: -0.57 (0.37), residues: 201 loop : -2.17 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP C 453 HIS 0.007 0.001 HIS A 731 PHE 0.014 0.002 PHE C 427 TYR 0.014 0.001 TYR A 663 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 73 time to evaluate : 0.627 Fit side-chains outliers start: 27 outliers final: 16 residues processed: 94 average time/residue: 0.1913 time to fit residues: 23.4384 Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 71 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 10.0000 chunk 33 optimal weight: 20.0000 chunk 7 optimal weight: 6.9990 chunk 30 optimal weight: 20.0000 chunk 42 optimal weight: 30.0000 chunk 63 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 20.0000 chunk 18 optimal weight: 9.9990 chunk 56 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 overall best weight: 5.6188 ------------------------------------------------------------------------------- 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: 0.8616 moved from start: 0.0911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 5852 Z= 0.302 Angle : 0.605 6.777 7974 Z= 0.318 Chirality : 0.047 0.165 856 Planarity : 0.005 0.050 1048 Dihedral : 4.747 22.610 786 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.17 % Favored : 91.83 % Rotamer: Outliers : 4.69 % Allowed : 18.45 % Favored : 76.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.46 (0.30), residues: 710 helix: -2.39 (0.57), residues: 66 sheet: -0.49 (0.37), residues: 201 loop : -2.18 (0.27), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 453 HIS 0.005 0.001 HIS A 731 PHE 0.011 0.001 PHE C 427 TYR 0.013 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 73 time to evaluate : 0.745 Fit side-chains REVERT: A 855 LEU cc_start: 0.8895 (OUTLIER) cc_final: 0.8563 (tt) REVERT: A 865 GLU cc_start: 0.7905 (pm20) cc_final: 0.7298 (pm20) outliers start: 29 outliers final: 20 residues processed: 96 average time/residue: 0.2002 time to fit residues: 25.4204 Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 69 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 800 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 10.0000 chunk 50 optimal weight: 7.9990 chunk 27 optimal weight: 8.9990 chunk 57 optimal weight: 9.9990 chunk 46 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 60 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 22 optimal weight: 9.9990 chunk 13 optimal weight: 0.0770 chunk 39 optimal weight: 5.9990 overall best weight: 5.2146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 713 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8612 moved from start: 0.1033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 5852 Z= 0.285 Angle : 0.599 7.119 7974 Z= 0.313 Chirality : 0.046 0.161 856 Planarity : 0.005 0.042 1048 Dihedral : 4.677 22.698 786 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.69 % Allowed : 18.93 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.42 (0.30), residues: 710 helix: -2.40 (0.58), residues: 66 sheet: -0.32 (0.37), residues: 197 loop : -2.20 (0.27), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 453 HIS 0.005 0.001 HIS A 731 PHE 0.011 0.001 PHE C 402 TYR 0.013 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 74 time to evaluate : 0.694 Fit side-chains REVERT: A 855 LEU cc_start: 0.8900 (OUTLIER) cc_final: 0.8568 (tt) outliers start: 29 outliers final: 23 residues processed: 97 average time/residue: 0.2088 time to fit residues: 26.2032 Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.686 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 458 THR Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 8.9990 chunk 67 optimal weight: 5.9990 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 10.0000 chunk 5 optimal weight: 0.9990 chunk 22 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 7 optimal weight: 3.9990 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 186 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8562 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5852 Z= 0.172 Angle : 0.543 6.730 7974 Z= 0.283 Chirality : 0.044 0.157 856 Planarity : 0.004 0.033 1048 Dihedral : 4.231 21.171 786 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.62 % Favored : 93.38 % Rotamer: Outliers : 3.07 % Allowed : 20.39 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.31 (0.30), residues: 710 helix: -2.25 (0.60), residues: 66 sheet: -0.37 (0.36), residues: 204 loop : -2.10 (0.27), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 453 HIS 0.003 0.001 HIS A 731 PHE 0.010 0.001 PHE C 402 TYR 0.012 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 71 time to evaluate : 0.739 Fit side-chains REVERT: A 812 TYR cc_start: 0.8764 (t80) cc_final: 0.8367 (t80) REVERT: C 419 VAL cc_start: 0.8875 (OUTLIER) cc_final: 0.8647 (t) outliers start: 19 outliers final: 15 residues processed: 86 average time/residue: 0.2085 time to fit residues: 22.9965 Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 63 time to evaluate : 0.649 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 229 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 419 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 10.0000 chunk 57 optimal weight: 10.0000 chunk 37 optimal weight: 0.2980 chunk 67 optimal weight: 8.9990 chunk 42 optimal weight: 5.9990 chunk 41 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 40 optimal weight: 7.9990 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 overall best weight: 3.8386 ------------------------------------------------------------------------------- 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: 0.8587 moved from start: 0.1273 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5852 Z= 0.232 Angle : 0.568 6.342 7974 Z= 0.298 Chirality : 0.045 0.157 856 Planarity : 0.005 0.062 1048 Dihedral : 4.312 21.670 786 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 3.88 % Allowed : 19.74 % Favored : 76.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.32 (0.30), residues: 710 helix: -2.27 (0.59), residues: 66 sheet: -0.50 (0.36), residues: 210 loop : -2.04 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 453 HIS 0.004 0.001 HIS A 731 PHE 0.010 0.001 PHE C 402 TYR 0.012 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 66 time to evaluate : 0.670 Fit side-chains REVERT: A 812 TYR cc_start: 0.8796 (t80) cc_final: 0.8292 (t80) REVERT: A 855 LEU cc_start: 0.8865 (OUTLIER) cc_final: 0.8463 (tt) REVERT: B 227 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9127 (tt) outliers start: 24 outliers final: 19 residues processed: 84 average time/residue: 0.2112 time to fit residues: 23.0191 Evaluate side-chains 85 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 64 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 227 LEU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 579 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 13 optimal weight: 2.9990 chunk 42 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 53 optimal weight: 7.9990 chunk 61 optimal weight: 8.9990 chunk 64 optimal weight: 20.0000 chunk 58 optimal weight: 6.9990 chunk 62 optimal weight: 7.9990 chunk 37 optimal weight: 0.0570 overall best weight: 4.8106 ------------------------------------------------------------------------------- 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: 0.8601 moved from start: 0.1203 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5852 Z= 0.270 Angle : 0.597 6.748 7974 Z= 0.314 Chirality : 0.046 0.157 856 Planarity : 0.005 0.059 1048 Dihedral : 4.431 22.140 786 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % Rotamer: Outliers : 4.37 % Allowed : 19.09 % Favored : 76.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.32 (0.30), residues: 710 helix: -2.29 (0.59), residues: 66 sheet: -0.48 (0.36), residues: 210 loop : -2.06 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 580 HIS 0.005 0.001 HIS A 731 PHE 0.011 0.001 PHE C 427 TYR 0.013 0.001 TYR B 150 ARG 0.002 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 65 time to evaluate : 0.661 Fit side-chains REVERT: A 812 TYR cc_start: 0.8804 (t80) cc_final: 0.8250 (t80) REVERT: A 855 LEU cc_start: 0.8864 (OUTLIER) cc_final: 0.8476 (tt) outliers start: 27 outliers final: 24 residues processed: 86 average time/residue: 0.1907 time to fit residues: 21.4999 Evaluate side-chains 88 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 63 time to evaluate : 0.736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 579 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 5.9990 chunk 49 optimal weight: 9.9990 chunk 19 optimal weight: 0.0050 chunk 56 optimal weight: 20.0000 chunk 59 optimal weight: 20.0000 chunk 62 optimal weight: 20.0000 chunk 41 optimal weight: 10.0000 chunk 66 optimal weight: 9.9990 chunk 40 optimal weight: 7.9990 chunk 31 optimal weight: 5.9990 chunk 46 optimal weight: 10.0000 overall best weight: 6.0002 ------------------------------------------------------------------------------- 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: 0.8617 moved from start: 0.1213 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5852 Z= 0.322 Angle : 0.623 7.053 7974 Z= 0.328 Chirality : 0.047 0.157 856 Planarity : 0.005 0.052 1048 Dihedral : 4.588 22.763 786 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 4.21 % Allowed : 19.58 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.34 (0.30), residues: 710 helix: -2.34 (0.58), residues: 66 sheet: -0.42 (0.36), residues: 208 loop : -2.10 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 580 HIS 0.005 0.001 HIS A 731 PHE 0.012 0.002 PHE C 493 TYR 0.014 0.001 TYR B 150 ARG 0.002 0.000 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 64 time to evaluate : 0.727 Fit side-chains REVERT: A 812 TYR cc_start: 0.8819 (t80) cc_final: 0.8255 (t80) REVERT: A 855 LEU cc_start: 0.8883 (OUTLIER) cc_final: 0.8508 (tt) outliers start: 26 outliers final: 25 residues processed: 83 average time/residue: 0.1966 time to fit residues: 21.2720 Evaluate side-chains 89 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 63 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 670 VAL Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 852 ILE Chi-restraints excluded: chain A residue 853 ASP Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 164 ASP Chi-restraints excluded: chain B residue 212 ILE Chi-restraints excluded: chain B residue 224 GLU Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 366 THR Chi-restraints excluded: chain C residue 373 ILE Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 443 VAL Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 493 PHE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 579 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 0.8980 chunk 64 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 5 optimal weight: 0.8980 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 59 optimal weight: 20.0000 chunk 17 optimal weight: 20.0000 chunk 51 optimal weight: 0.0020 chunk 8 optimal weight: 1.9990 overall best weight: 1.1592 ------------------------------------------------------------------------------- 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: 0.8541 moved from start: 0.1524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.043 5852 Z= 0.159 Angle : 0.545 7.383 7974 Z= 0.283 Chirality : 0.043 0.154 856 Planarity : 0.004 0.044 1048 Dihedral : 4.041 20.489 786 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 2.59 % Allowed : 21.36 % Favored : 76.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.21 (0.30), residues: 710 helix: -2.16 (0.61), residues: 66 sheet: -0.43 (0.36), residues: 210 loop : -1.98 (0.28), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 453 HIS 0.003 0.001 HIS B 176 PHE 0.009 0.001 PHE A 753 TYR 0.011 0.001 TYR B 150 ARG 0.003 0.000 ARG B 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1420 Ramachandran restraints generated. 710 Oldfield, 0 Emsley, 710 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 66 time to evaluate : 0.650 Fit side-chains REVERT: A 812 TYR cc_start: 0.8719 (t80) cc_final: 0.8378 (t80) REVERT: A 855 LEU cc_start: 0.8839 (OUTLIER) cc_final: 0.8361 (tt) outliers start: 16 outliers final: 14 residues processed: 77 average time/residue: 0.2225 time to fit residues: 21.8370 Evaluate side-chains 79 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 64 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 669 LEU Chi-restraints excluded: chain A residue 683 THR Chi-restraints excluded: chain A residue 789 LEU Chi-restraints excluded: chain A residue 832 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain B residue 109 THR Chi-restraints excluded: chain B residue 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 336 VAL Chi-restraints excluded: chain C residue 378 ILE Chi-restraints excluded: chain C residue 475 ILE Chi-restraints excluded: chain C residue 508 THR Chi-restraints excluded: chain C residue 510 GLU Chi-restraints excluded: chain C residue 578 VAL Chi-restraints excluded: chain C residue 579 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 10.0000 chunk 55 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 9.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 0.0870 chunk 48 optimal weight: 30.0000 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 20.0000 chunk 63 optimal weight: 0.0010 chunk 37 optimal weight: 0.0030 overall best weight: 1.8178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.097476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3009 r_free = 0.3009 target = 0.080964 restraints weight = 9913.224| |-----------------------------------------------------------------------------| r_work (start): 0.3009 rms_B_bonded: 2.32 r_work: 0.2906 rms_B_bonded: 2.66 restraints_weight: 0.5000 r_work: 0.2791 rms_B_bonded: 4.40 restraints_weight: 0.2500 r_work (final): 0.2791 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8521 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5852 Z= 0.173 Angle : 0.552 9.817 7974 Z= 0.287 Chirality : 0.043 0.152 856 Planarity : 0.004 0.063 1048 Dihedral : 3.948 20.331 786 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 4.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.63 % Favored : 94.37 % Rotamer: Outliers : 3.40 % Allowed : 20.39 % Favored : 76.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % 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: -2.13 (0.30), residues: 710 helix: -2.10 (0.61), residues: 66 sheet: -0.31 (0.36), residues: 208 loop : -1.95 (0.28), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 453 HIS 0.003 0.001 HIS A 731 PHE 0.010 0.001 PHE C 402 TYR 0.017 0.001 TYR A 777 ARG 0.004 0.000 ARG B 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1453.39 seconds wall clock time: 27 minutes 29.26 seconds (1649.26 seconds total)