Starting phenix.real_space_refine on Tue Feb 3 22:22:31 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9lcz_62997/02_2026/9lcz_62997.cif Found real_map, /net/cci-nas-00/data/ceres_data/9lcz_62997/02_2026/9lcz_62997.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.93 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9lcz_62997/02_2026/9lcz_62997.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9lcz_62997/02_2026/9lcz_62997.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9lcz_62997/02_2026/9lcz_62997.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9lcz_62997/02_2026/9lcz_62997.map" } resolution = 2.93 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= 0.001 sd= 0.156 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: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 58 5.49 5 S 21 5.16 5 C 4407 2.51 5 N 1330 2.21 5 O 1514 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5952/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 7331 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6141 Number of conformers: 1 Conformer: "" Number of residues, atoms: 834, 6141 Classifications: {'peptide': 834} Link IDs: {'PTRANS': 46, 'TRANS': 787} Chain: "B" Number of atoms: 589 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 589 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "C" Number of atoms: 600 Number of conformers: 1 Conformer: "" Number of residues, atoms: 29, 600 Classifications: {'DNA': 29} Link IDs: {'rna3p': 28} Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 5824 SG CYS A 842 32.870 51.504 29.524 1.00 59.71 S ATOM 5846 SG CYS A 845 35.256 50.719 25.775 1.00 35.38 S Time building chain proxies: 1.79, per 1000 atoms: 0.24 Number of scatterers: 7331 At special positions: 0 Unit cell: (85.1067, 84.0294, 127.121, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 21 16.00 P 58 15.00 O 1514 8.00 N 1330 7.00 C 4407 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: 0.79 Conformation dependent library (CDL) restraints added in 249.1 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" ND1 HIS A 814 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 842 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 845 " 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1512 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 1 sheets defined 74.5% alpha, 3.5% beta 24 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 0.82 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 63 through 81 removed outlier: 3.587A pdb=" N LEU A 67 " --> pdb=" O HIS A 63 " (cutoff:3.500A) removed outlier: 3.622A pdb=" N GLY A 68 " --> pdb=" O PRO A 64 " (cutoff:3.500A) removed outlier: 6.767A pdb=" N GLN A 75 " --> pdb=" O ALA A 71 " (cutoff:3.500A) removed outlier: 6.491A pdb=" N ASP A 76 " --> pdb=" O VAL A 72 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N MET A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA A 79 " --> pdb=" O GLN A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 97 through 113 removed outlier: 4.973A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N GLU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ARG A 113 " --> pdb=" O ALA A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'A' and resid 132 through 142 Processing helix chain 'A' and resid 142 through 147 removed outlier: 3.956A pdb=" N THR A 147 " --> pdb=" O ARG A 143 " (cutoff:3.500A) Processing helix chain 'A' and resid 154 through 163 Processing helix chain 'A' and resid 166 through 184 removed outlier: 3.651A pdb=" N ALA A 170 " --> pdb=" O GLY A 166 " (cutoff:3.500A) Proline residue: A 179 - end of helix Processing helix chain 'A' and resid 188 through 197 Processing helix chain 'A' and resid 200 through 219 Proline residue: A 213 - end of helix removed outlier: 3.536A pdb=" N HIS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 230 Processing helix chain 'A' and resid 234 through 252 Proline residue: A 247 - end of helix Processing helix chain 'A' and resid 256 through 265 Processing helix chain 'A' and resid 268 through 286 Proline residue: A 281 - end of helix Processing helix chain 'A' and resid 290 through 299 Processing helix chain 'A' and resid 302 through 320 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 324 through 332 Processing helix chain 'A' and resid 336 through 354 Proline residue: A 349 - end of helix Processing helix chain 'A' and resid 358 through 367 Processing helix chain 'A' and resid 370 through 388 Proline residue: A 383 - end of helix Processing helix chain 'A' and resid 392 through 401 Processing helix chain 'A' and resid 404 through 422 Proline residue: A 417 - end of helix Processing helix chain 'A' and resid 426 through 435 Processing helix chain 'A' and resid 438 through 456 Proline residue: A 451 - end of helix Processing helix chain 'A' and resid 460 through 469 Processing helix chain 'A' and resid 472 through 490 Proline residue: A 485 - end of helix Processing helix chain 'A' and resid 494 through 504 removed outlier: 4.576A pdb=" N HIS A 504 " --> pdb=" O ALA A 500 " (cutoff:3.500A) Processing helix chain 'A' and resid 506 through 524 Proline residue: A 519 - end of helix Processing helix chain 'A' and resid 528 through 537 Processing helix chain 'A' and resid 540 through 558 Proline residue: A 553 - end of helix Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 574 through 593 Proline residue: A 587 - end of helix removed outlier: 3.502A pdb=" N HIS A 593 " --> pdb=" O LEU A 589 " (cutoff:3.500A) Processing helix chain 'A' and resid 596 through 605 Processing helix chain 'A' and resid 608 through 626 Proline residue: A 621 - end of helix Processing helix chain 'A' and resid 630 through 639 Processing helix chain 'A' and resid 642 through 660 Proline residue: A 655 - end of helix Processing helix chain 'A' and resid 664 through 673 removed outlier: 3.502A pdb=" N VAL A 668 " --> pdb=" O THR A 664 " (cutoff:3.500A) Processing helix chain 'A' and resid 676 through 690 Processing helix chain 'A' and resid 692 through 703 Processing helix chain 'A' and resid 715 through 734 Processing helix chain 'A' and resid 738 through 752 Processing helix chain 'A' and resid 803 through 807 removed outlier: 3.663A pdb=" N THR A 807 " --> pdb=" O PRO A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 843 through 849 removed outlier: 4.036A pdb=" N THR A 847 " --> pdb=" O GLY A 843 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N THR A 849 " --> pdb=" O CYS A 845 " (cutoff:3.500A) Processing helix chain 'A' and resid 850 through 852 No H-bonds generated for 'chain 'A' and resid 850 through 852' Processing sheet with id=AA1, first strand: chain 'A' and resid 765 through 768 removed outlier: 4.441A pdb=" N ALA A 708 " --> pdb=" O GLY A 796 " (cutoff:3.500A) removed outlier: 6.979A pdb=" N ALA A 831 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 8.010A pdb=" N VAL A 862 " --> pdb=" O ALA A 831 " (cutoff:3.500A) removed outlier: 6.521A pdb=" N VAL A 833 " --> pdb=" O VAL A 862 " (cutoff:3.500A) 398 hydrogen bonds defined for protein. 1179 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 58 hydrogen bonds 116 hydrogen bond angles 0 basepair planarities 24 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.09 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1730 1.33 - 1.45: 1578 1.45 - 1.57: 4122 1.57 - 1.69: 114 1.69 - 1.81: 25 Bond restraints: 7569 Sorted by residual: bond pdb=" N ASN A 812 " pdb=" CA ASN A 812 " ideal model delta sigma weight residual 1.456 1.493 -0.036 1.28e-02 6.10e+03 8.04e+00 bond pdb=" N TYR A 809 " pdb=" CA TYR A 809 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.30e-02 5.92e+03 7.30e+00 bond pdb=" N ASN A 811 " pdb=" CA ASN A 811 " ideal model delta sigma weight residual 1.455 1.490 -0.035 1.33e-02 5.65e+03 6.95e+00 bond pdb=" N ASN A 808 " pdb=" CA ASN A 808 " ideal model delta sigma weight residual 1.459 1.491 -0.033 1.25e-02 6.40e+03 6.76e+00 bond pdb=" N THR A 664 " pdb=" CA THR A 664 " ideal model delta sigma weight residual 1.452 1.488 -0.036 1.41e-02 5.03e+03 6.59e+00 ... (remaining 7564 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.60: 10193 1.60 - 3.20: 290 3.20 - 4.81: 34 4.81 - 6.41: 36 6.41 - 8.01: 11 Bond angle restraints: 10564 Sorted by residual: angle pdb=" N GLU A 698 " pdb=" CA GLU A 698 " pdb=" CB GLU A 698 " ideal model delta sigma weight residual 110.16 115.60 -5.44 1.48e+00 4.57e-01 1.35e+01 angle pdb=" C ASN A 812 " pdb=" N GLY A 813 " pdb=" CA GLY A 813 " ideal model delta sigma weight residual 121.85 127.84 -5.99 1.76e+00 3.23e-01 1.16e+01 angle pdb=" N ASN A 811 " pdb=" CA ASN A 811 " pdb=" C ASN A 811 " ideal model delta sigma weight residual 113.30 108.91 4.39 1.34e+00 5.57e-01 1.08e+01 angle pdb=" CB ARG A 176 " pdb=" CG ARG A 176 " pdb=" CD ARG A 176 " ideal model delta sigma weight residual 111.30 118.46 -7.16 2.30e+00 1.89e-01 9.68e+00 angle pdb=" CA THR A 664 " pdb=" C THR A 664 " pdb=" N PRO A 665 " ideal model delta sigma weight residual 117.67 120.81 -3.14 1.01e+00 9.80e-01 9.66e+00 ... (remaining 10559 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.66: 3653 16.66 - 33.33: 476 33.33 - 49.99: 193 49.99 - 66.66: 85 66.66 - 83.32: 8 Dihedral angle restraints: 4415 sinusoidal: 2060 harmonic: 2355 Sorted by residual: dihedral pdb=" CA THR A 107 " pdb=" C THR A 107 " pdb=" N VAL A 108 " pdb=" CA VAL A 108 " ideal model delta harmonic sigma weight residual -180.00 -164.36 -15.64 0 5.00e+00 4.00e-02 9.78e+00 dihedral pdb=" CG ARG A 210 " pdb=" CD ARG A 210 " pdb=" NE ARG A 210 " pdb=" CZ ARG A 210 " ideal model delta sinusoidal sigma weight residual 90.00 130.79 -40.79 2 1.50e+01 4.44e-03 9.11e+00 dihedral pdb=" CA GLU A 292 " pdb=" CB GLU A 292 " pdb=" CG GLU A 292 " pdb=" CD GLU A 292 " ideal model delta sinusoidal sigma weight residual 60.00 109.32 -49.32 3 1.50e+01 4.44e-03 8.76e+00 ... (remaining 4412 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.121: 1262 0.121 - 0.242: 3 0.242 - 0.363: 1 0.363 - 0.484: 0 0.484 - 0.605: 9 Chirality restraints: 1275 Sorted by residual: chirality pdb=" P DC C -3 " pdb=" OP1 DC C -3 " pdb=" OP2 DC C -3 " pdb=" O5' DC C -3 " both_signs ideal model delta sigma weight residual True 2.35 -2.95 -0.60 2.00e-01 2.50e+01 9.14e+00 chirality pdb=" P DC B 1 " pdb=" OP1 DC B 1 " pdb=" OP2 DC B 1 " pdb=" O5' DC B 1 " both_signs ideal model delta sigma weight residual True 2.35 -2.92 -0.57 2.00e-01 2.50e+01 8.23e+00 chirality pdb=" P DC B -13 " pdb=" OP1 DC B -13 " pdb=" OP2 DC B -13 " pdb=" O5' DC B -13 " both_signs ideal model delta sigma weight residual True 2.35 -2.90 -0.56 2.00e-01 2.50e+01 7.73e+00 ... (remaining 1272 not shown) Planarity restraints: 1179 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 660 " 0.020 2.00e-02 2.50e+03 3.94e-02 1.55e+01 pdb=" C ALA A 660 " -0.068 2.00e-02 2.50e+03 pdb=" O ALA A 660 " 0.026 2.00e-02 2.50e+03 pdb=" N HIS A 661 " 0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 810 " -0.009 2.00e-02 2.50e+03 1.92e-02 3.70e+00 pdb=" C ARG A 810 " 0.033 2.00e-02 2.50e+03 pdb=" O ARG A 810 " -0.012 2.00e-02 2.50e+03 pdb=" N ASN A 811 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " 0.031 5.00e-02 4.00e+02 4.67e-02 3.49e+00 pdb=" N PRO A 427 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.026 5.00e-02 4.00e+02 ... (remaining 1176 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1050 2.76 - 3.29: 6780 3.29 - 3.83: 12732 3.83 - 4.36: 15353 4.36 - 4.90: 25475 Nonbonded interactions: 61390 Sorted by model distance: nonbonded pdb=" O VAL A 329 " pdb=" OG SER A 333 " model vdw 2.223 3.040 nonbonded pdb=" O VAL A 295 " pdb=" OG SER A 299 " model vdw 2.259 3.040 nonbonded pdb=" NH1 ARG A 702 " pdb=" OG1 THR A 782 " model vdw 2.298 3.120 nonbonded pdb=" O GLY A 800 " pdb=" NZ LYS A 818 " model vdw 2.298 3.120 nonbonded pdb=" O CYS A 845 " pdb=" OG1 THR A 849 " model vdw 2.319 3.040 ... (remaining 61385 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: 1.060 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: 0.020 Set scattering table: 0.020 Process input model: 9.750 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:6.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7973 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 : 0.006 0.289 7572 Z= 0.250 Angle : 0.711 8.011 10564 Z= 0.370 Chirality : 0.061 0.605 1275 Planarity : 0.005 0.047 1179 Dihedral : 18.655 83.322 2903 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.00 % Allowed : 0.15 % Favored : 99.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.81 (0.29), residues: 832 helix: 0.97 (0.22), residues: 577 sheet: 0.85 (0.71), residues: 47 loop : -0.56 (0.40), residues: 208 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 678 TYR 0.007 0.001 TYR A 697 PHE 0.003 0.001 PHE A 52 TRP 0.005 0.001 TRP A 773 HIS 0.003 0.001 HIS A 504 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 7569) covalent geometry : angle 0.71051 (10564) hydrogen bonds : bond 0.14568 ( 456) hydrogen bonds : angle 5.99223 ( 1295) metal coordination : bond 0.17246 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 85 time to evaluate : 0.245 Fit side-chains REVERT: A 702 ARG cc_start: 0.8340 (mtp85) cc_final: 0.8121 (mtp180) REVERT: A 721 THR cc_start: 0.8392 (m) cc_final: 0.8065 (p) outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.5936 time to fit residues: 53.3755 Evaluate side-chains 58 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.248 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 49 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 38 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 74 optimal weight: 0.5980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 157 GLN A 175 GLN A 625 GLN A 659 GLN A 871 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.193673 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3989 r_free = 0.3989 target = 0.187301 restraints weight = 5939.455| |-----------------------------------------------------------------------------| r_work (start): 0.3993 rms_B_bonded: 0.45 r_work: 0.3726 rms_B_bonded: 1.03 restraints_weight: 0.5000 r_work: 0.3579 rms_B_bonded: 2.08 restraints_weight: 0.2500 r_work: 0.3436 rms_B_bonded: 4.51 restraints_weight: 0.1250 r_work (final): 0.3436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7959 moved from start: 0.1257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 7572 Z= 0.169 Angle : 0.575 6.378 10564 Z= 0.308 Chirality : 0.040 0.119 1275 Planarity : 0.004 0.047 1179 Dihedral : 21.026 82.342 1495 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 5.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.22 % Allowed : 8.81 % Favored : 89.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.99 (0.29), residues: 832 helix: 1.09 (0.22), residues: 582 sheet: 0.56 (0.71), residues: 50 loop : -0.38 (0.43), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 702 TYR 0.007 0.001 TYR A 697 PHE 0.002 0.001 PHE A 768 TRP 0.006 0.001 TRP A 773 HIS 0.004 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7569) covalent geometry : angle 0.57548 (10564) hydrogen bonds : bond 0.03799 ( 456) hydrogen bonds : angle 4.24075 ( 1295) metal coordination : bond 0.00588 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 57 time to evaluate : 0.264 Fit side-chains REVERT: A 721 THR cc_start: 0.8098 (m) cc_final: 0.7835 (p) outliers start: 8 outliers final: 4 residues processed: 62 average time/residue: 0.5717 time to fit residues: 37.5451 Evaluate side-chains 56 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 562 THR Chi-restraints excluded: chain A residue 762 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 8 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 39 optimal weight: 0.9990 chunk 56 optimal weight: 0.8980 chunk 34 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 17 optimal weight: 0.3980 chunk 80 optimal weight: 0.8980 chunk 43 optimal weight: 0.1980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 225 GLN A 871 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4059 r_free = 0.4059 target = 0.194603 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.186457 restraints weight = 5888.069| |-----------------------------------------------------------------------------| r_work (start): 0.3990 rms_B_bonded: 0.56 r_work: 0.3700 rms_B_bonded: 1.31 restraints_weight: 0.5000 r_work: 0.3580 rms_B_bonded: 3.45 restraints_weight: 0.2500 r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7572 Z= 0.142 Angle : 0.529 6.288 10564 Z= 0.284 Chirality : 0.039 0.121 1275 Planarity : 0.004 0.050 1179 Dihedral : 20.871 80.248 1495 Min Nonbonded Distance : 2.514 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.82 % Allowed : 10.64 % Favored : 87.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.29 (0.29), residues: 832 helix: 1.33 (0.22), residues: 581 sheet: 0.88 (0.75), residues: 47 loop : -0.35 (0.43), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 143 TYR 0.009 0.001 TYR A 697 PHE 0.001 0.000 PHE A 52 TRP 0.009 0.001 TRP A 773 HIS 0.003 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 7569) covalent geometry : angle 0.52886 (10564) hydrogen bonds : bond 0.03071 ( 456) hydrogen bonds : angle 3.98777 ( 1295) metal coordination : bond 0.00247 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 55 time to evaluate : 0.174 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 60 average time/residue: 0.5447 time to fit residues: 34.7991 Evaluate side-chains 57 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 52 time to evaluate : 0.242 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 0.9990 chunk 41 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 1 optimal weight: 0.5980 chunk 70 optimal weight: 0.0980 chunk 74 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 24 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 625 GLN A 659 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.193784 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3978 r_free = 0.3978 target = 0.185557 restraints weight = 6022.857| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 0.57 r_work: 0.3696 rms_B_bonded: 1.29 restraints_weight: 0.5000 r_work: 0.3535 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3535 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7879 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7572 Z= 0.148 Angle : 0.537 6.359 10564 Z= 0.288 Chirality : 0.039 0.121 1275 Planarity : 0.004 0.051 1179 Dihedral : 20.872 79.732 1495 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 4.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 1.82 % Allowed : 12.46 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.17 (0.29), residues: 832 helix: 1.25 (0.22), residues: 586 sheet: 0.86 (0.75), residues: 47 loop : -0.49 (0.45), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 143 TYR 0.008 0.001 TYR A 697 PHE 0.001 0.000 PHE A 52 TRP 0.006 0.001 TRP A 142 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00332 ( 7569) covalent geometry : angle 0.53742 (10564) hydrogen bonds : bond 0.03129 ( 456) hydrogen bonds : angle 4.01013 ( 1295) metal coordination : bond 0.00246 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.248 Fit side-chains outliers start: 12 outliers final: 7 residues processed: 58 average time/residue: 0.5116 time to fit residues: 31.5616 Evaluate side-chains 55 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 64 optimal weight: 0.8980 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 1 optimal weight: 0.0980 chunk 73 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 chunk 50 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 overall best weight: 0.7384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN A 659 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4047 r_free = 0.4047 target = 0.193292 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.186151 restraints weight = 5973.469| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 0.50 r_work: 0.3711 rms_B_bonded: 1.11 restraints_weight: 0.5000 r_work: 0.3565 rms_B_bonded: 2.06 restraints_weight: 0.2500 r_work: 0.3414 rms_B_bonded: 4.61 restraints_weight: 0.1250 r_work (final): 0.3414 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7982 moved from start: 0.1713 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7572 Z= 0.150 Angle : 0.534 6.390 10564 Z= 0.287 Chirality : 0.039 0.118 1275 Planarity : 0.004 0.051 1179 Dihedral : 20.873 80.116 1495 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 4.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 1.52 % Allowed : 14.13 % Favored : 84.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.24 (0.29), residues: 832 helix: 1.29 (0.22), residues: 585 sheet: 0.95 (0.76), residues: 47 loop : -0.44 (0.44), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG A 143 TYR 0.009 0.001 TYR A 697 PHE 0.001 0.000 PHE A 852 TRP 0.010 0.001 TRP A 142 HIS 0.004 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00339 ( 7569) covalent geometry : angle 0.53439 (10564) hydrogen bonds : bond 0.03152 ( 456) hydrogen bonds : angle 4.02339 ( 1295) metal coordination : bond 0.00285 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.248 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 60 average time/residue: 0.5201 time to fit residues: 33.3187 Evaluate side-chains 59 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 52 time to evaluate : 0.256 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 29 optimal weight: 0.5980 chunk 13 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 61 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 140 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4052 r_free = 0.4052 target = 0.193724 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3979 r_free = 0.3979 target = 0.185613 restraints weight = 5932.402| |-----------------------------------------------------------------------------| r_work (start): 0.3983 rms_B_bonded: 0.56 r_work: 0.3692 rms_B_bonded: 1.28 restraints_weight: 0.5000 r_work: 0.3522 rms_B_bonded: 2.98 restraints_weight: 0.2500 r_work (final): 0.3522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.1808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 7572 Z= 0.146 Angle : 0.530 6.395 10564 Z= 0.286 Chirality : 0.039 0.130 1275 Planarity : 0.004 0.050 1179 Dihedral : 20.813 80.381 1495 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.82 % Allowed : 14.59 % Favored : 83.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.29), residues: 832 helix: 1.32 (0.22), residues: 583 sheet: 0.99 (0.77), residues: 47 loop : -0.48 (0.44), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 143 TYR 0.009 0.001 TYR A 697 PHE 0.001 0.000 PHE A 852 TRP 0.012 0.002 TRP A 142 HIS 0.005 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 7569) covalent geometry : angle 0.53044 (10564) hydrogen bonds : bond 0.03029 ( 456) hydrogen bonds : angle 3.99080 ( 1295) metal coordination : bond 0.00257 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 54 time to evaluate : 0.241 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 61 average time/residue: 0.5575 time to fit residues: 36.1816 Evaluate side-chains 60 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 4.9990 chunk 23 optimal weight: 0.1980 chunk 66 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 0.7980 chunk 32 optimal weight: 0.4980 chunk 36 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 175 GLN A 625 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.193971 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.185987 restraints weight = 6003.806| |-----------------------------------------------------------------------------| r_work (start): 0.3984 rms_B_bonded: 0.55 r_work: 0.3702 rms_B_bonded: 1.26 restraints_weight: 0.5000 r_work: 0.3537 rms_B_bonded: 3.09 restraints_weight: 0.2500 r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7869 moved from start: 0.1837 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7572 Z= 0.141 Angle : 0.526 6.394 10564 Z= 0.284 Chirality : 0.039 0.134 1275 Planarity : 0.004 0.048 1179 Dihedral : 20.742 80.327 1495 Min Nonbonded Distance : 2.394 Molprobity Statistics. All-atom Clashscore : 4.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.82 % Allowed : 14.29 % Favored : 83.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.34 (0.29), residues: 832 helix: 1.36 (0.22), residues: 582 sheet: 1.06 (0.77), residues: 47 loop : -0.40 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 143 TYR 0.009 0.001 TYR A 697 PHE 0.001 0.000 PHE A 852 TRP 0.013 0.002 TRP A 142 HIS 0.005 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00314 ( 7569) covalent geometry : angle 0.52583 (10564) hydrogen bonds : bond 0.02958 ( 456) hydrogen bonds : angle 3.98576 ( 1295) metal coordination : bond 0.00244 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.151 Fit side-chains REVERT: A 60 LEU cc_start: 0.8133 (OUTLIER) cc_final: 0.7765 (mp) REVERT: A 455 GLN cc_start: 0.8098 (OUTLIER) cc_final: 0.7751 (tm-30) outliers start: 12 outliers final: 9 residues processed: 61 average time/residue: 0.5103 time to fit residues: 33.0219 Evaluate side-chains 65 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 54 time to evaluate : 0.239 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 58 optimal weight: 3.9990 chunk 5 optimal weight: 4.9990 chunk 68 optimal weight: 0.4980 chunk 49 optimal weight: 0.9990 chunk 79 optimal weight: 3.9990 chunk 51 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 63 optimal weight: 0.8980 chunk 57 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 chunk 10 optimal weight: 0.0050 overall best weight: 0.4994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 140 HIS A 175 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.194755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.4000 r_free = 0.4000 target = 0.187660 restraints weight = 6011.995| |-----------------------------------------------------------------------------| r_work (start): 0.4002 rms_B_bonded: 0.50 r_work: 0.3730 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3582 rms_B_bonded: 2.16 restraints_weight: 0.2500 r_work: 0.3445 rms_B_bonded: 4.48 restraints_weight: 0.1250 r_work (final): 0.3445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7942 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7572 Z= 0.134 Angle : 0.526 6.390 10564 Z= 0.284 Chirality : 0.038 0.134 1275 Planarity : 0.004 0.048 1179 Dihedral : 20.641 80.091 1495 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.28 % Allowed : 14.74 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.38 (0.29), residues: 832 helix: 1.39 (0.22), residues: 581 sheet: 1.14 (0.77), residues: 47 loop : -0.38 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.000 ARG A 143 TYR 0.009 0.001 TYR A 697 PHE 0.001 0.000 PHE A 852 TRP 0.016 0.002 TRP A 142 HIS 0.003 0.001 HIS A 140 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 7569) covalent geometry : angle 0.52581 (10564) hydrogen bonds : bond 0.02796 ( 456) hydrogen bonds : angle 3.94398 ( 1295) metal coordination : bond 0.00192 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.184 Fit side-chains REVERT: A 60 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7691 (mp) REVERT: A 455 GLN cc_start: 0.8183 (OUTLIER) cc_final: 0.7830 (tm-30) outliers start: 15 outliers final: 10 residues processed: 63 average time/residue: 0.5247 time to fit residues: 35.1132 Evaluate side-chains 62 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 50 time to evaluate : 0.251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 455 GLN Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 711 ILE Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 745 VAL Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 11 optimal weight: 3.9990 chunk 76 optimal weight: 0.7980 chunk 41 optimal weight: 0.8980 chunk 19 optimal weight: 0.3980 chunk 51 optimal weight: 0.9990 chunk 60 optimal weight: 0.9980 chunk 13 optimal weight: 0.9980 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 2 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 625 GLN A 812 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4043 r_free = 0.4043 target = 0.192923 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3977 r_free = 0.3977 target = 0.185659 restraints weight = 5929.750| |-----------------------------------------------------------------------------| r_work (start): 0.3980 rms_B_bonded: 0.51 r_work: 0.3700 rms_B_bonded: 1.17 restraints_weight: 0.5000 r_work: 0.3540 rms_B_bonded: 2.57 restraints_weight: 0.2500 r_work (final): 0.3540 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.1872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 7572 Z= 0.161 Angle : 0.556 7.366 10564 Z= 0.298 Chirality : 0.040 0.134 1275 Planarity : 0.004 0.054 1179 Dihedral : 20.839 79.777 1495 Min Nonbonded Distance : 2.409 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 2.13 % Allowed : 14.89 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.13 (0.29), residues: 832 helix: 1.27 (0.22), residues: 582 sheet: 1.02 (0.78), residues: 47 loop : -0.69 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 143 TYR 0.009 0.001 TYR A 697 PHE 0.001 0.000 PHE A 852 TRP 0.015 0.002 TRP A 142 HIS 0.003 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00368 ( 7569) covalent geometry : angle 0.55584 (10564) hydrogen bonds : bond 0.03238 ( 456) hydrogen bonds : angle 4.08116 ( 1295) metal coordination : bond 0.00317 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 53 time to evaluate : 0.248 Fit side-chains REVERT: A 60 LEU cc_start: 0.8113 (OUTLIER) cc_final: 0.7766 (mp) outliers start: 14 outliers final: 7 residues processed: 61 average time/residue: 0.4906 time to fit residues: 31.9293 Evaluate side-chains 60 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 52 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 23 optimal weight: 0.9990 chunk 83 optimal weight: 1.9990 chunk 57 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 62 optimal weight: 0.7980 chunk 39 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 67 optimal weight: 0.5980 chunk 38 optimal weight: 0.7980 chunk 6 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN A 812 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4063 r_free = 0.4063 target = 0.194754 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3997 r_free = 0.3997 target = 0.187482 restraints weight = 5940.897| |-----------------------------------------------------------------------------| r_work (start): 0.4001 rms_B_bonded: 0.51 r_work: 0.3725 rms_B_bonded: 1.19 restraints_weight: 0.5000 r_work: 0.3560 rms_B_bonded: 2.74 restraints_weight: 0.2500 r_work: 0.3441 rms_B_bonded: 4.57 restraints_weight: 0.1250 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7947 moved from start: 0.1999 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7572 Z= 0.135 Angle : 0.531 8.263 10564 Z= 0.287 Chirality : 0.038 0.135 1275 Planarity : 0.004 0.057 1179 Dihedral : 20.610 79.912 1495 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 5.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 1.37 % Allowed : 15.65 % Favored : 82.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.35 (0.29), residues: 832 helix: 1.42 (0.22), residues: 581 sheet: 1.12 (0.78), residues: 47 loop : -0.54 (0.44), residues: 204 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.000 ARG A 143 TYR 0.009 0.001 TYR A 697 PHE 0.002 0.000 PHE A 52 TRP 0.015 0.002 TRP A 142 HIS 0.003 0.000 HIS A 470 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 7569) covalent geometry : angle 0.53148 (10564) hydrogen bonds : bond 0.02775 ( 456) hydrogen bonds : angle 3.97635 ( 1295) metal coordination : bond 0.00195 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1664 Ramachandran restraints generated. 832 Oldfield, 0 Emsley, 832 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.246 Fit side-chains REVERT: A 60 LEU cc_start: 0.8093 (OUTLIER) cc_final: 0.7714 (mp) REVERT: A 102 LEU cc_start: 0.8075 (OUTLIER) cc_final: 0.7677 (mt) REVERT: A 258 GLU cc_start: 0.7627 (tp30) cc_final: 0.7414 (mp0) outliers start: 9 outliers final: 7 residues processed: 60 average time/residue: 0.5088 time to fit residues: 32.5901 Evaluate side-chains 61 residues out of total 658 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 52 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 102 LEU Chi-restraints excluded: chain A residue 174 VAL Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 LEU Chi-restraints excluded: chain A residue 551 LEU Chi-restraints excluded: chain A residue 725 LEU Chi-restraints excluded: chain A residue 762 SER Chi-restraints excluded: chain A residue 878 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 79 optimal weight: 3.9990 chunk 80 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 71 optimal weight: 0.7980 chunk 64 optimal weight: 0.8980 chunk 83 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 chunk 5 optimal weight: 0.5980 chunk 18 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 175 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4044 r_free = 0.4044 target = 0.192988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 23)----------------| | r_work = 0.3981 r_free = 0.3981 target = 0.185880 restraints weight = 5910.303| |-----------------------------------------------------------------------------| r_work (start): 0.3982 rms_B_bonded: 0.50 r_work: 0.3703 rms_B_bonded: 1.15 restraints_weight: 0.5000 r_work: 0.3544 rms_B_bonded: 2.64 restraints_weight: 0.2500 r_work (final): 0.3544 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7866 moved from start: 0.1946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 7572 Z= 0.160 Angle : 0.559 8.180 10564 Z= 0.300 Chirality : 0.040 0.135 1275 Planarity : 0.004 0.056 1179 Dihedral : 20.820 79.849 1495 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.67 % Allowed : 15.65 % Favored : 82.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.29), residues: 832 helix: 1.26 (0.22), residues: 582 sheet: 0.92 (0.76), residues: 47 loop : -0.69 (0.44), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG A 143 TYR 0.010 0.001 TYR A 697 PHE 0.002 0.001 PHE A 52 TRP 0.016 0.002 TRP A 142 HIS 0.003 0.001 HIS A 661 Details of bonding type rmsd covalent geometry : bond 0.00367 ( 7569) covalent geometry : angle 0.55895 (10564) hydrogen bonds : bond 0.03212 ( 456) hydrogen bonds : angle 4.10155 ( 1295) metal coordination : bond 0.00317 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2217.31 seconds wall clock time: 38 minutes 36.48 seconds (2316.48 seconds total)