Starting phenix.real_space_refine on Fri Aug 22 16:12:39 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8b3j_15830/08_2025/8b3j_15830.cif Found real_map, /net/cci-nas-00/data/ceres_data/8b3j_15830/08_2025/8b3j_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_15830/08_2025/8b3j_15830.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8b3j_15830/08_2025/8b3j_15830.map" model { file = "/net/cci-nas-00/data/ceres_data/8b3j_15830/08_2025/8b3j_15830.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8b3j_15830/08_2025/8b3j_15830.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.032 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: 1.51, per 1000 atoms: 0.27 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: 0.40 Conformation dependent library (CDL) restraints added in 247.5 milliseconds Enol-peptide restraints added in 953.7 nanoseconds 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: 0.20 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: 0.88 Time building geometry restraints manager: 0.58 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: 3.060 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: 0.120 Check model and map are aligned: 0.030 Set scattering table: 0.010 Process input model: 7.500 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.140 ------------------------------------------------------------------------------- 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= 0.194 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -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 ARG 0.003 0.000 ARG A 698 TYR 0.013 0.001 TYR A 663 PHE 0.015 0.002 PHE C 402 TRP 0.010 0.001 TRP C 453 HIS 0.004 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00468 ( 5852) covalent geometry : angle 0.62954 ( 7974) hydrogen bonds : bond 0.22429 ( 135) hydrogen bonds : angle 7.32899 ( 381) *********************** 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 : 0.230 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: 0.0970 time to fit residues: 8.8633 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 : 0.227 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 49 optimal weight: 9.9990 chunk 53 optimal weight: 8.9990 chunk 5 optimal weight: 3.9990 chunk 33 optimal weight: 20.0000 chunk 65 optimal weight: 7.9990 chunk 62 optimal weight: 0.0270 chunk 51 optimal weight: 20.0000 chunk 38 optimal weight: 5.9990 chunk 61 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 chunk 27 optimal weight: 8.9990 overall best weight: 2.7644 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.095818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2998 r_free = 0.2998 target = 0.079787 restraints weight = 10048.429| |-----------------------------------------------------------------------------| r_work (start): 0.2996 rms_B_bonded: 2.28 r_work: 0.2897 rms_B_bonded: 2.59 restraints_weight: 0.5000 r_work: 0.2782 rms_B_bonded: 4.31 restraints_weight: 0.2500 r_work (final): 0.2782 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8584 moved from start: 0.0747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5852 Z= 0.120 Angle : 0.561 6.685 7974 Z= 0.295 Chirality : 0.045 0.174 856 Planarity : 0.004 0.055 1048 Dihedral : 4.460 21.130 786 Min Nonbonded Distance : 2.590 Molprobity Statistics. All-atom Clashscore : 3.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.18 % Favored : 92.82 % Rotamer: Outliers : 2.43 % Allowed : 18.12 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.54 (0.30), residues: 710 helix: -2.33 (0.57), residues: 71 sheet: -0.73 (0.36), residues: 208 loop : -2.15 (0.27), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG C 333 TYR 0.011 0.001 TYR B 150 PHE 0.008 0.001 PHE C 581 TRP 0.010 0.001 TRP C 453 HIS 0.004 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 5852) covalent geometry : angle 0.56102 ( 7974) hydrogen bonds : bond 0.04395 ( 135) hydrogen bonds : angle 5.50307 ( 381) *********************** 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 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.221 Fit side-chains REVERT: A 812 TYR cc_start: 0.8846 (t80) cc_final: 0.8194 (t80) REVERT: B 234 LYS cc_start: 0.8587 (mttm) cc_final: 0.8140 (mmtm) outliers start: 15 outliers final: 9 residues processed: 88 average time/residue: 0.0827 time to fit residues: 9.2438 Evaluate side-chains 77 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 68 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 257 VAL Chi-restraints excluded: chain C residue 333 ARG Chi-restraints excluded: chain C residue 386 ASP 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 12 optimal weight: 3.9990 chunk 10 optimal weight: 9.9990 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 32 optimal weight: 7.9990 chunk 46 optimal weight: 10.0000 chunk 42 optimal weight: 30.0000 chunk 7 optimal weight: 7.9990 chunk 49 optimal weight: 9.9990 chunk 43 optimal weight: 8.9990 chunk 36 optimal weight: 20.0000 overall best weight: 6.1990 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.093294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2962 r_free = 0.2962 target = 0.077651 restraints weight = 10047.079| |-----------------------------------------------------------------------------| r_work (start): 0.2964 rms_B_bonded: 2.23 r_work: 0.2862 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2749 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2749 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.0818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5852 Z= 0.197 Angle : 0.604 7.004 7974 Z= 0.317 Chirality : 0.047 0.176 856 Planarity : 0.005 0.057 1048 Dihedral : 4.697 22.354 786 Min Nonbonded Distance : 2.585 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer: Outliers : 3.88 % Allowed : 18.28 % Favored : 77.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.96 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.30), residues: 710 helix: -2.20 (0.59), residues: 65 sheet: -0.70 (0.36), residues: 210 loop : -2.12 (0.27), residues: 435 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 698 TYR 0.013 0.001 TYR B 150 PHE 0.013 0.002 PHE C 427 TRP 0.011 0.001 TRP C 453 HIS 0.006 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00487 ( 5852) covalent geometry : angle 0.60380 ( 7974) hydrogen bonds : bond 0.04548 ( 135) hydrogen bonds : angle 5.46824 ( 381) *********************** 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 98 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 74 time to evaluate : 0.236 Fit side-chains REVERT: A 865 GLU cc_start: 0.8020 (pm20) cc_final: 0.7814 (pm20) outliers start: 24 outliers final: 17 residues processed: 92 average time/residue: 0.0812 time to fit residues: 9.7225 Evaluate side-chains 90 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 73 time to evaluate : 0.145 ------------------------------------------------------------------------------- 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 852 ILE 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 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 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 57 optimal weight: 9.9990 chunk 45 optimal weight: 10.0000 chunk 38 optimal weight: 8.9990 chunk 60 optimal weight: 20.0000 chunk 13 optimal weight: 5.9990 chunk 56 optimal weight: 10.0000 chunk 54 optimal weight: 0.2980 chunk 14 optimal weight: 6.9990 chunk 55 optimal weight: 3.9990 chunk 39 optimal weight: 7.9990 chunk 33 optimal weight: 20.0000 overall best weight: 5.0588 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.093948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2974 r_free = 0.2974 target = 0.078335 restraints weight = 10125.190| |-----------------------------------------------------------------------------| r_work (start): 0.2975 rms_B_bonded: 2.22 r_work: 0.2872 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.2757 rms_B_bonded: 4.24 restraints_weight: 0.2500 r_work (final): 0.2757 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8613 moved from start: 0.0917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5852 Z= 0.167 Angle : 0.588 6.592 7974 Z= 0.309 Chirality : 0.046 0.164 856 Planarity : 0.005 0.042 1048 Dihedral : 4.602 22.095 786 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.32 % Favored : 92.68 % Rotamer: Outliers : 4.21 % Allowed : 18.93 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.47 (0.30), residues: 710 helix: -2.21 (0.58), residues: 67 sheet: -0.63 (0.36), residues: 210 loop : -2.16 (0.27), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.012 0.001 TYR B 150 PHE 0.011 0.001 PHE C 427 TRP 0.010 0.001 TRP C 453 HIS 0.005 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00415 ( 5852) covalent geometry : angle 0.58781 ( 7974) hydrogen bonds : bond 0.04100 ( 135) hydrogen bonds : angle 5.36814 ( 381) *********************** 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 100 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 74 time to evaluate : 0.164 Fit side-chains REVERT: A 855 LEU cc_start: 0.8921 (OUTLIER) cc_final: 0.8583 (tt) REVERT: A 865 GLU cc_start: 0.8019 (pm20) cc_final: 0.7417 (pm20) outliers start: 26 outliers final: 18 residues processed: 93 average time/residue: 0.0742 time to fit residues: 9.0197 Evaluate side-chains 83 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 64 time to evaluate : 0.244 ------------------------------------------------------------------------------- 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 164 ASP 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 373 ILE 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 21 optimal weight: 6.9990 chunk 63 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 47 optimal weight: 9.9990 chunk 15 optimal weight: 9.9990 chunk 55 optimal weight: 10.0000 chunk 4 optimal weight: 20.0000 chunk 14 optimal weight: 9.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 overall best weight: 8.5990 ------------------------------------------------------------------------------- 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 = 0.3191 r_free = 0.3191 target = 0.092070 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2940 r_free = 0.2940 target = 0.076370 restraints weight = 10339.549| |-----------------------------------------------------------------------------| r_work (start): 0.2941 rms_B_bonded: 2.24 r_work: 0.2838 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2725 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8651 moved from start: 0.1005 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.049 5852 Z= 0.262 Angle : 0.671 7.195 7974 Z= 0.352 Chirality : 0.049 0.166 856 Planarity : 0.005 0.042 1048 Dihedral : 4.980 23.399 786 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 4.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 4.85 % Allowed : 18.61 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.45 (0.29), residues: 710 helix: -2.36 (0.56), residues: 67 sheet: -0.29 (0.37), residues: 197 loop : -2.27 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.016 0.002 TYR A 663 PHE 0.015 0.002 PHE C 493 TRP 0.012 0.002 TRP C 453 HIS 0.007 0.002 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00652 ( 5852) covalent geometry : angle 0.67093 ( 7974) hydrogen bonds : bond 0.04764 ( 135) hydrogen bonds : angle 5.50373 ( 381) *********************** 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 96 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 66 time to evaluate : 0.227 Fit side-chains REVERT: A 855 LEU cc_start: 0.8920 (OUTLIER) cc_final: 0.8603 (tt) REVERT: C 403 GLU cc_start: 0.8148 (OUTLIER) cc_final: 0.7397 (pp20) outliers start: 30 outliers final: 20 residues processed: 91 average time/residue: 0.0888 time to fit residues: 10.4173 Evaluate side-chains 87 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 65 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 164 ASP Chi-restraints excluded: chain B residue 212 ILE 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 378 ILE Chi-restraints excluded: chain C residue 403 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 7 optimal weight: 7.9990 chunk 55 optimal weight: 3.9990 chunk 53 optimal weight: 6.9990 chunk 8 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 32 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 29 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 4.7990 ------------------------------------------------------------------------------- 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 = 0.3219 r_free = 0.3219 target = 0.093799 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2969 r_free = 0.2969 target = 0.078068 restraints weight = 10079.695| |-----------------------------------------------------------------------------| r_work (start): 0.2970 rms_B_bonded: 2.23 r_work: 0.2869 rms_B_bonded: 2.55 restraints_weight: 0.5000 r_work: 0.2754 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.2754 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1059 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5852 Z= 0.162 Angle : 0.590 6.508 7974 Z= 0.309 Chirality : 0.046 0.161 856 Planarity : 0.004 0.037 1048 Dihedral : 4.677 22.400 786 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 4.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.44 (0.30), residues: 710 helix: -2.25 (0.58), residues: 67 sheet: -0.43 (0.36), residues: 206 loop : -2.22 (0.27), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.013 0.001 TYR B 150 PHE 0.010 0.001 PHE C 402 TRP 0.011 0.001 TRP C 453 HIS 0.005 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00403 ( 5852) covalent geometry : angle 0.59002 ( 7974) hydrogen bonds : bond 0.03974 ( 135) hydrogen bonds : angle 5.33346 ( 381) *********************** 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 91 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 65 time to evaluate : 0.195 Fit side-chains REVERT: A 855 LEU cc_start: 0.8903 (OUTLIER) cc_final: 0.8519 (tt) outliers start: 26 outliers final: 18 residues processed: 84 average time/residue: 0.0976 time to fit residues: 10.4675 Evaluate side-chains 80 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.237 ------------------------------------------------------------------------------- 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 832 LEU Chi-restraints excluded: chain A residue 855 LEU Chi-restraints excluded: chain A residue 892 VAL Chi-restraints excluded: chain B residue 188 LYS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 4 optimal weight: 20.0000 chunk 23 optimal weight: 6.9990 chunk 9 optimal weight: 2.9990 chunk 57 optimal weight: 10.0000 chunk 53 optimal weight: 5.9990 chunk 35 optimal weight: 9.9990 chunk 6 optimal weight: 8.9990 chunk 16 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 overall best weight: 5.7990 ------------------------------------------------------------------------------- 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 = 0.3215 r_free = 0.3215 target = 0.093567 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2958 r_free = 0.2958 target = 0.077421 restraints weight = 10154.670| |-----------------------------------------------------------------------------| r_work (start): 0.2957 rms_B_bonded: 2.28 r_work: 0.2856 rms_B_bonded: 2.58 restraints_weight: 0.5000 r_work: 0.2740 rms_B_bonded: 4.26 restraints_weight: 0.2500 r_work (final): 0.2740 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 5852 Z= 0.187 Angle : 0.608 6.628 7974 Z= 0.319 Chirality : 0.047 0.159 856 Planarity : 0.005 0.038 1048 Dihedral : 4.701 22.734 786 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.61 % Favored : 92.39 % Rotamer: Outliers : 4.85 % Allowed : 19.09 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -2.40 (0.30), residues: 710 helix: -2.29 (0.58), residues: 67 sheet: -0.27 (0.37), residues: 197 loop : -2.22 (0.27), residues: 446 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG B 92 TYR 0.013 0.001 TYR B 150 PHE 0.011 0.002 PHE C 427 TRP 0.010 0.001 TRP C 453 HIS 0.005 0.001 HIS A 731 Details of bonding type rmsd covalent geometry : bond 0.00465 ( 5852) covalent geometry : angle 0.60795 ( 7974) hydrogen bonds : bond 0.04140 ( 135) hydrogen bonds : angle 5.34310 ( 381) *********************** 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 93 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 63 time to evaluate : 0.238 Fit side-chains REVERT: A 812 TYR cc_start: 0.8881 (t80) cc_final: 0.8318 (t80) outliers start: 30 outliers final: 23 residues processed: 87 average time/residue: 0.0886 time to fit residues: 10.0505 Evaluate side-chains 84 residues out of total 618 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 61 time to evaluate : 0.231 ------------------------------------------------------------------------------- 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 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 164 ASP Chi-restraints excluded: chain B residue 188 LYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/command_line/real_space_refine.py", line 9, in run_program(real_space_refine.Program) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/iotbx/cli_parser.py", line 999, in run_program task.run() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/programs/real_space_refine.py", line 206, in run self.rsr_result = rsr_wrappers.run_real_space_refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/rsr/wrappers.py", line 52, in __init__ self._refined = macro_cycle_real_space.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/phenix/refinement/macro_cycle_real_space.py", line 755, in minimization_no_ncs ro = mmtbx.refinement.real_space.individual_sites.easy( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 44, in __init__ self.weight = mmtbx.refinement.real_space.weight.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/weight.py", line 84, in __init__ ro.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 362, in refine real_space_result = refinery( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 233, in __init__ refiner.refine( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/mmtbx/refinement/real_space/individual_sites.py", line 100, in refine self.refined = maptbx.real_space_refinement_simple.lbfgs( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 168, in __init__ O.minimizer = scitbx.lbfgs.run( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 270, in run return run_c_plus_plus( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/maptbx/real_space_refinement_simple.py", line 243, in compute_functional_and_gradients gr_e = O.geometry_restraints_manager.energies_sites( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1588, in energies_sites pair_proxies = self.pair_proxies( File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1491, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/cctbx/geometry_restraints/manager.py", line 1372, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 54.6205 > 50: distance: 32 - 41: 11.919 distance: 41 - 42: 6.625 distance: 42 - 43: 4.905 distance: 42 - 45: 18.289 distance: 43 - 44: 13.285 distance: 43 - 49: 14.723 distance: 45 - 46: 11.442 distance: 46 - 47: 13.047 distance: 46 - 48: 12.433 distance: 49 - 50: 26.888 distance: 50 - 51: 11.983 distance: 50 - 53: 40.015 distance: 51 - 52: 49.207 distance: 51 - 56: 50.759 distance: 53 - 54: 15.549 distance: 53 - 55: 23.801 distance: 56 - 57: 16.044 distance: 57 - 58: 14.533 distance: 57 - 60: 15.145 distance: 58 - 59: 37.134 distance: 58 - 64: 18.207 distance: 60 - 61: 24.980 distance: 61 - 62: 23.014 distance: 61 - 63: 21.817 distance: 64 - 65: 34.315 distance: 65 - 66: 22.717 distance: 65 - 68: 20.284 distance: 66 - 67: 21.673 distance: 66 - 72: 15.593 distance: 68 - 69: 21.860 distance: 69 - 70: 25.442 distance: 69 - 71: 37.611 distance: 72 - 73: 24.047 distance: 73 - 74: 40.507 distance: 73 - 76: 18.354 distance: 74 - 75: 46.728 distance: 74 - 83: 21.249 distance: 75 - 278: 31.838 distance: 76 - 77: 19.435 distance: 77 - 78: 30.764 distance: 77 - 79: 24.350 distance: 78 - 80: 29.304 distance: 79 - 81: 10.494 distance: 80 - 82: 33.093 distance: 81 - 82: 35.575 distance: 83 - 84: 9.719 distance: 83 - 205: 18.917 distance: 84 - 85: 39.096 distance: 84 - 87: 28.218 distance: 85 - 86: 21.530 distance: 85 - 95: 43.393 distance: 87 - 88: 16.324 distance: 88 - 89: 21.168 distance: 88 - 90: 19.283 distance: 89 - 91: 11.758 distance: 90 - 92: 10.369 distance: 91 - 93: 7.333 distance: 92 - 93: 7.239 distance: 93 - 94: 8.466 distance: 95 - 96: 15.249 distance: 95 - 269: 23.947 distance: 96 - 97: 20.032 distance: 96 - 99: 22.251 distance: 97 - 98: 11.716 distance: 97 - 102: 6.227 distance: 98 - 266: 17.049 distance: 99 - 100: 23.302 distance: 99 - 101: 31.877 distance: 102 - 103: 38.510 distance: 103 - 104: 30.945 distance: 103 - 106: 5.424 distance: 104 - 105: 8.301 distance: 104 - 112: 26.241 distance: 106 - 107: 26.470 distance: 107 - 108: 47.272 distance: 107 - 109: 30.172 distance: 108 - 110: 33.601 distance: 109 - 111: 33.866 distance: 110 - 111: 16.870 distance: 112 - 113: 30.973 distance: 113 - 114: 33.274 distance: 113 - 116: 33.057 distance: 114 - 115: 28.656 distance: 114 - 119: 8.936 distance: 116 - 117: 41.796 distance: 116 - 118: 9.895 distance: 119 - 120: 23.272 distance: 120 - 121: 24.199 distance: 120 - 123: 16.176 distance: 121 - 122: 37.958 distance: 121 - 129: 28.024 distance: 123 - 124: 24.805 distance: 124 - 125: 14.436 distance: 124 - 126: 9.461 distance: 125 - 127: 22.909 distance: 126 - 128: 16.134 distance: 127 - 128: 9.391