Starting phenix.real_space_refine on Tue Feb 3 21:59:59 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9ld0_62998/02_2026/9ld0_62998_neut.cif Found real_map, /net/cci-nas-00/data/ceres_data/9ld0_62998/02_2026/9ld0_62998.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9ld0_62998/02_2026/9ld0_62998_neut.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9ld0_62998/02_2026/9ld0_62998_neut.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9ld0_62998/02_2026/9ld0_62998.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9ld0_62998/02_2026/9ld0_62998.map" } resolution = 3.17 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= 0.000 sd= 0.107 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 54 5.49 5 S 21 5.16 5 C 4359 2.51 5 N 1313 2.21 5 O 1484 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 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: 7232 Number of models: 1 Model: "" Number of chains: 4 Chain: "B" Number of atoms: 549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 549 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "C" Number of atoms: 558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 27, 558 Classifications: {'DNA': 27} Link IDs: {'rna3p': 26} Chain: "A" Number of atoms: 6124 Number of conformers: 1 Conformer: "" Number of residues, atoms: 832, 6124 Classifications: {'peptide': 832} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 785} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 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 6957 SG CYS A 845 33.009 52.323 26.451 1.00 47.15 S Time building chain proxies: 1.48, per 1000 atoms: 0.20 Number of scatterers: 7232 At special positions: 0 Unit cell: (81.8748, 84.0294, 129.276, 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 54 15.00 O 1484 8.00 N 1313 7.00 C 4359 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: 0.76 Conformation dependent library (CDL) restraints added in 257.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A 901 " pdb="ZN ZN A 901 " - pdb=" SG CYS A 845 " pdb="ZN ZN A 901 " - pdb=" NE2 HIS A 814 " 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1508 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 1 sheets defined 75.0% alpha, 2.2% beta 27 base pairs and 47 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 53 through 61 Processing helix chain 'A' and resid 62 through 64 No H-bonds generated for 'chain 'A' and resid 62 through 64' Processing helix chain 'A' and resid 65 through 73 removed outlier: 3.921A pdb=" N THR A 69 " --> pdb=" O ALA A 65 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ALA A 71 " --> pdb=" O LEU A 67 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LYS A 73 " --> pdb=" O THR A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 73 through 81 removed outlier: 3.722A pdb=" N MET A 77 " --> pdb=" O LYS A 73 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ILE A 78 " --> pdb=" O TYR A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 94 Processing helix chain 'A' and resid 97 through 113 removed outlier: 5.256A pdb=" N GLY A 110 " --> pdb=" O LEU A 106 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N GLU A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) removed outlier: 3.731A 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: 3.800A 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 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 removed outlier: 3.652A pdb=" N ALA A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 213 - end of helix removed outlier: 3.568A pdb=" N HIS A 219 " --> pdb=" O LEU A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 222 through 231 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 298 Processing helix chain 'A' and resid 302 through 320 Proline residue: A 315 - end of helix Processing helix chain 'A' and resid 324 through 333 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 390 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 502 Processing helix chain 'A' and resid 506 through 525 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 removed outlier: 3.644A pdb=" N ALA A 544 " --> pdb=" O GLY A 540 " (cutoff:3.500A) Proline residue: A 553 - end of helix Processing helix chain 'A' and resid 562 through 571 Processing helix chain 'A' and resid 574 through 592 Proline residue: A 587 - end of helix 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 Processing helix chain 'A' and resid 676 through 690 removed outlier: 3.804A pdb=" N ALA A 680 " --> pdb=" O GLY A 676 " (cutoff:3.500A) Processing helix chain 'A' and resid 692 through 703 removed outlier: 3.719A pdb=" N LEU A 703 " --> pdb=" O ALA A 699 " (cutoff:3.500A) Processing helix chain 'A' and resid 715 through 733 removed outlier: 3.733A pdb=" N ILE A 719 " --> pdb=" O SER A 715 " (cutoff:3.500A) Processing helix chain 'A' and resid 737 through 752 removed outlier: 4.055A pdb=" N ASP A 741 " --> pdb=" O LEU A 737 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ILE A 742 " --> pdb=" O SER A 738 " (cutoff:3.500A) Processing helix chain 'A' and resid 803 through 807 Processing helix chain 'A' and resid 814 through 827 Processing helix chain 'A' and resid 844 through 853 removed outlier: 4.301A pdb=" N ALA A 850 " --> pdb=" O ASN A 846 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 794 through 798 removed outlier: 6.856A pdb=" N ALA A 831 " --> pdb=" O THR A 860 " (cutoff:3.500A) removed outlier: 8.418A pdb=" N VAL A 862 " --> pdb=" O ALA A 831 " (cutoff:3.500A) removed outlier: 6.657A pdb=" N VAL A 833 " --> pdb=" O VAL A 862 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N VAL A 861 " --> pdb=" O LYS A 879 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N LYS A 879 " --> pdb=" O VAL A 861 " (cutoff:3.500A) 385 hydrogen bonds defined for protein. 1146 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 69 hydrogen bonds 138 hydrogen bond angles 0 basepair planarities 27 basepair parallelities 47 stacking parallelities Total time for adding SS restraints: 1.72 Time building geometry restraints manager: 0.97 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: 2199 1.34 - 1.46: 1188 1.46 - 1.58: 3942 1.58 - 1.70: 106 1.70 - 1.82: 25 Bond restraints: 7460 Sorted by residual: bond pdb=" N ILE A 709 " pdb=" CA ILE A 709 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.19e-02 7.06e+03 9.15e+00 bond pdb=" N ILE A 711 " pdb=" CA ILE A 711 " ideal model delta sigma weight residual 1.456 1.495 -0.039 1.30e-02 5.92e+03 9.03e+00 bond pdb=" N THR A 841 " pdb=" CA THR A 841 " ideal model delta sigma weight residual 1.456 1.489 -0.033 1.23e-02 6.61e+03 7.07e+00 bond pdb=" N CYS A 842 " pdb=" CA CYS A 842 " ideal model delta sigma weight residual 1.454 1.489 -0.035 1.34e-02 5.57e+03 6.90e+00 bond pdb=" N ARG A 710 " pdb=" CA ARG A 710 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.29e-02 6.01e+03 5.39e+00 ... (remaining 7455 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.67: 10203 1.67 - 3.33: 159 3.33 - 5.00: 27 5.00 - 6.67: 9 6.67 - 8.33: 1 Bond angle restraints: 10399 Sorted by residual: angle pdb=" CA ILE A 711 " pdb=" C ILE A 711 " pdb=" O ILE A 711 " ideal model delta sigma weight residual 121.58 117.97 3.61 1.00e+00 1.00e+00 1.30e+01 angle pdb=" CA CYS A 842 " pdb=" C CYS A 842 " pdb=" O CYS A 842 " ideal model delta sigma weight residual 121.87 118.35 3.52 1.16e+00 7.43e-01 9.19e+00 angle pdb=" CA SER A 712 " pdb=" C SER A 712 " pdb=" O SER A 712 " ideal model delta sigma weight residual 121.49 118.01 3.48 1.16e+00 7.43e-01 8.99e+00 angle pdb=" CA THR A 841 " pdb=" C THR A 841 " pdb=" O THR A 841 " ideal model delta sigma weight residual 121.19 118.03 3.16 1.10e+00 8.26e-01 8.23e+00 angle pdb=" CA ARG A 710 " pdb=" C ARG A 710 " pdb=" O ARG A 710 " ideal model delta sigma weight residual 121.34 117.98 3.36 1.18e+00 7.18e-01 8.11e+00 ... (remaining 10394 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 33.59: 4021 33.59 - 67.19: 325 67.19 - 100.78: 12 100.78 - 134.37: 0 134.37 - 167.97: 2 Dihedral angle restraints: 4360 sinusoidal: 2011 harmonic: 2349 Sorted by residual: dihedral pdb=" CA ARG A 448 " pdb=" C ARG A 448 " pdb=" N LEU A 449 " pdb=" CA LEU A 449 " ideal model delta harmonic sigma weight residual -180.00 -159.46 -20.54 0 5.00e+00 4.00e-02 1.69e+01 dihedral pdb=" C4' DC B -13 " pdb=" C3' DC B -13 " pdb=" O3' DC B -13 " pdb=" P DC B -12 " ideal model delta sinusoidal sigma weight residual 220.00 52.03 167.97 1 3.50e+01 8.16e-04 1.55e+01 dihedral pdb=" C4' DC B -10 " pdb=" C3' DC B -10 " pdb=" O3' DC B -10 " pdb=" P DA B -9 " ideal model delta sinusoidal sigma weight residual 220.00 65.04 154.96 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 4357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 924 0.038 - 0.077: 240 0.077 - 0.115: 84 0.115 - 0.153: 6 0.153 - 0.191: 2 Chirality restraints: 1256 Sorted by residual: chirality pdb=" CA ILE A 711 " pdb=" N ILE A 711 " pdb=" C ILE A 711 " pdb=" CB ILE A 711 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.14e-01 chirality pdb=" CA ILE A 709 " pdb=" N ILE A 709 " pdb=" C ILE A 709 " pdb=" CB ILE A 709 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.16 2.00e-01 2.50e+01 6.20e-01 chirality pdb=" P DC B -12 " pdb=" OP1 DC B -12 " pdb=" OP2 DC B -12 " pdb=" O5' DC B -12 " both_signs ideal model delta sigma weight residual True 2.35 -2.48 -0.14 2.00e-01 2.50e+01 4.56e-01 ... (remaining 1253 not shown) Planarity restraints: 1172 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 392 " 0.029 5.00e-02 4.00e+02 4.46e-02 3.19e+00 pdb=" N PRO A 393 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 393 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 393 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 562 " -0.027 5.00e-02 4.00e+02 4.15e-02 2.75e+00 pdb=" N PRO A 563 " 0.072 5.00e-02 4.00e+02 pdb=" CA PRO A 563 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 563 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 426 " 0.027 5.00e-02 4.00e+02 4.03e-02 2.60e+00 pdb=" N PRO A 427 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO A 427 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 427 " 0.023 5.00e-02 4.00e+02 ... (remaining 1169 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 81 2.66 - 3.22: 6433 3.22 - 3.78: 11857 3.78 - 4.34: 15214 4.34 - 4.90: 24856 Nonbonded interactions: 58441 Sorted by model distance: nonbonded pdb=" CG HIS A 814 " pdb="ZN ZN A 901 " model vdw 2.097 1.960 nonbonded pdb=" OG1 THR A 596 " pdb=" OE1 GLN A 599 " model vdw 2.200 3.040 nonbonded pdb=" O VAL A 363 " pdb=" OG SER A 367 " model vdw 2.257 3.040 nonbonded pdb=" O GLN A 441 " pdb=" OG1 THR A 445 " model vdw 2.281 3.040 nonbonded pdb=" O VAL A 397 " pdb=" OG SER A 401 " model vdw 2.285 3.040 ... (remaining 58436 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: 1.610 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: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.170 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:1.410 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 13.390 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6540 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 0.322 7462 Z= 0.200 Angle : 0.552 8.332 10399 Z= 0.308 Chirality : 0.039 0.191 1256 Planarity : 0.004 0.045 1172 Dihedral : 20.414 167.967 2852 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % 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: 830 helix: 1.49 (0.23), residues: 558 sheet: -0.95 (0.96), residues: 30 loop : -0.59 (0.36), residues: 242 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 702 TYR 0.015 0.001 TYR A 697 PHE 0.004 0.001 PHE A 852 TRP 0.007 0.001 TRP A 773 HIS 0.002 0.000 HIS A 766 Details of bonding type rmsd covalent geometry : bond 0.00283 ( 7460) covalent geometry : angle 0.55210 (10399) hydrogen bonds : bond 0.14645 ( 454) hydrogen bonds : angle 5.16805 ( 1284) metal coordination : bond 0.22783 ( 2) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 101 time to evaluate : 0.149 Fit side-chains REVERT: A 319 GLN cc_start: 0.7684 (tm-30) cc_final: 0.7336 (mm110) outliers start: 0 outliers final: 0 residues processed: 101 average time/residue: 0.0711 time to fit residues: 10.2440 Evaluate side-chains 63 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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: 2.9990 chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 65 optimal weight: 0.2980 chunk 62 optimal weight: 2.9990 chunk 51 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 61 optimal weight: 0.0870 chunk 45 optimal weight: 0.8980 chunk 74 optimal weight: 0.5980 overall best weight: 0.4758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 583 GLN A 817 GLN A 827 ASN A 835 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4247 r_free = 0.4247 target = 0.200398 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.181892 restraints weight = 7017.500| |-----------------------------------------------------------------------------| r_work (start): 0.4087 rms_B_bonded: 0.59 r_work: 0.3709 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3568 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3568 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2158 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7462 Z= 0.131 Angle : 0.554 8.269 10399 Z= 0.289 Chirality : 0.040 0.161 1256 Planarity : 0.004 0.046 1172 Dihedral : 21.762 164.647 1449 Min Nonbonded Distance : 1.802 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.53 % Allowed : 7.94 % Favored : 90.53 % 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: 1.11 (0.29), residues: 830 helix: 1.38 (0.21), residues: 583 sheet: -0.96 (0.81), residues: 42 loop : -0.63 (0.40), residues: 205 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 584 TYR 0.007 0.001 TYR A 881 PHE 0.010 0.001 PHE A 852 TRP 0.003 0.001 TRP A 96 HIS 0.006 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 7460) covalent geometry : angle 0.55409 (10399) hydrogen bonds : bond 0.02478 ( 454) hydrogen bonds : angle 4.04159 ( 1284) metal coordination : bond 0.00215 ( 2) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 60 time to evaluate : 0.240 Fit side-chains REVERT: A 319 GLN cc_start: 0.7938 (tm-30) cc_final: 0.7455 (mm110) REVERT: A 803 ASP cc_start: 0.3915 (t70) cc_final: 0.3343 (t70) outliers start: 10 outliers final: 3 residues processed: 67 average time/residue: 0.0659 time to fit residues: 6.6832 Evaluate side-chains 56 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 53 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 4 optimal weight: 0.0980 chunk 41 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 77 optimal weight: 10.0000 chunk 75 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 68 optimal weight: 0.6980 chunk 80 optimal weight: 10.0000 chunk 25 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 217 GLN A 253 HIS A 491 HIS A 835 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4165 r_free = 0.4165 target = 0.193109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4024 r_free = 0.4024 target = 0.176463 restraints weight = 6920.013| |-----------------------------------------------------------------------------| r_work (start): 0.4023 rms_B_bonded: 0.55 r_work: 0.3656 rms_B_bonded: 1.47 restraints_weight: 0.5000 r_work: 0.3454 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3454 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7981 moved from start: 0.3193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7462 Z= 0.162 Angle : 0.578 7.611 10399 Z= 0.302 Chirality : 0.041 0.138 1256 Planarity : 0.004 0.045 1172 Dihedral : 22.275 168.302 1449 Min Nonbonded Distance : 1.678 Molprobity Statistics. All-atom Clashscore : 6.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 1.98 % Allowed : 10.23 % Favored : 87.79 % 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: 0.98 (0.29), residues: 830 helix: 1.33 (0.22), residues: 582 sheet: -0.44 (0.78), residues: 45 loop : -0.95 (0.40), residues: 203 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 414 TYR 0.009 0.001 TYR A 697 PHE 0.005 0.001 PHE A 852 TRP 0.003 0.001 TRP A 96 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00376 ( 7460) covalent geometry : angle 0.57790 (10399) hydrogen bonds : bond 0.03315 ( 454) hydrogen bonds : angle 4.03593 ( 1284) metal coordination : bond 0.00342 ( 2) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.231 Fit side-chains REVERT: A 56 HIS cc_start: 0.7441 (OUTLIER) cc_final: 0.7213 (m-70) outliers start: 13 outliers final: 8 residues processed: 69 average time/residue: 0.0621 time to fit residues: 6.4391 Evaluate side-chains 62 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 53 time to evaluate : 0.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 791 ASP Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 44 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 9.9990 chunk 83 optimal weight: 8.9990 chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 80 optimal weight: 4.9990 chunk 21 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 835 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4137 r_free = 0.4137 target = 0.190242 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3970 r_free = 0.3970 target = 0.170839 restraints weight = 7004.111| |-----------------------------------------------------------------------------| r_work (start): 0.3965 rms_B_bonded: 0.59 r_work: 0.3512 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3370 rms_B_bonded: 4.30 restraints_weight: 0.2500 r_work (final): 0.3370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.3648 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 7462 Z= 0.220 Angle : 0.625 7.134 10399 Z= 0.327 Chirality : 0.042 0.124 1256 Planarity : 0.005 0.050 1172 Dihedral : 22.392 165.687 1449 Min Nonbonded Distance : 1.668 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 2.14 % Allowed : 12.37 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z 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: 0.79 (0.28), residues: 830 helix: 1.13 (0.21), residues: 585 sheet: -0.26 (0.77), residues: 45 loop : -0.93 (0.40), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 584 TYR 0.011 0.001 TYR A 697 PHE 0.008 0.001 PHE A 52 TRP 0.003 0.001 TRP A 96 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00527 ( 7460) covalent geometry : angle 0.62480 (10399) hydrogen bonds : bond 0.03641 ( 454) hydrogen bonds : angle 4.14909 ( 1284) metal coordination : bond 0.00286 ( 2) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 58 time to evaluate : 0.160 Fit side-chains REVERT: A 769 PRO cc_start: 0.7697 (Cg_endo) cc_final: 0.7494 (Cg_exo) REVERT: A 822 TYR cc_start: 0.7842 (t80) cc_final: 0.7492 (t80) outliers start: 14 outliers final: 12 residues processed: 67 average time/residue: 0.0617 time to fit residues: 6.0995 Evaluate side-chains 65 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 53 time to evaluate : 0.220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 385 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 775 LEU Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 78 optimal weight: 6.9990 chunk 64 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 82 optimal weight: 9.9990 chunk 9 optimal weight: 0.8980 chunk 57 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 28 optimal weight: 0.0030 chunk 59 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 63 HIS A 835 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4167 r_free = 0.4167 target = 0.192895 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.175513 restraints weight = 7045.750| |-----------------------------------------------------------------------------| r_work (start): 0.4019 rms_B_bonded: 0.55 r_work: 0.3658 rms_B_bonded: 1.45 restraints_weight: 0.5000 r_work: 0.3467 rms_B_bonded: 2.73 restraints_weight: 0.2500 r_work (final): 0.3467 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.3683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7462 Z= 0.135 Angle : 0.540 7.134 10399 Z= 0.283 Chirality : 0.039 0.131 1256 Planarity : 0.005 0.050 1172 Dihedral : 22.038 165.063 1449 Min Nonbonded Distance : 1.763 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.68 % Allowed : 12.98 % Favored : 85.34 % 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: 1.04 (0.29), residues: 830 helix: 1.33 (0.21), residues: 583 sheet: -0.15 (0.77), residues: 45 loop : -0.87 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 678 TYR 0.012 0.001 TYR A 778 PHE 0.005 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00304 ( 7460) covalent geometry : angle 0.53987 (10399) hydrogen bonds : bond 0.02661 ( 454) hydrogen bonds : angle 4.00615 ( 1284) metal coordination : bond 0.00142 ( 2) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 57 time to evaluate : 0.244 Fit side-chains REVERT: A 76 ASP cc_start: 0.7743 (m-30) cc_final: 0.7461 (t0) REVERT: A 769 PRO cc_start: 0.7814 (Cg_endo) cc_final: 0.7608 (Cg_exo) REVERT: A 822 TYR cc_start: 0.8001 (t80) cc_final: 0.7701 (t80) outliers start: 11 outliers final: 5 residues processed: 64 average time/residue: 0.0665 time to fit residues: 6.4362 Evaluate side-chains 60 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 756 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 61 optimal weight: 0.0470 chunk 8 optimal weight: 3.9990 chunk 30 optimal weight: 1.9990 chunk 72 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 chunk 2 optimal weight: 5.9990 chunk 80 optimal weight: 0.0980 chunk 54 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.6080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 835 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4175 r_free = 0.4175 target = 0.193506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 73)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.176069 restraints weight = 7049.251| |-----------------------------------------------------------------------------| r_work (start): 0.4025 rms_B_bonded: 0.55 r_work: 0.3675 rms_B_bonded: 1.37 restraints_weight: 0.5000 r_work: 0.3474 rms_B_bonded: 3.28 restraints_weight: 0.2500 r_work (final): 0.3474 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7961 moved from start: 0.3795 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7462 Z= 0.131 Angle : 0.533 6.802 10399 Z= 0.280 Chirality : 0.039 0.131 1256 Planarity : 0.005 0.050 1172 Dihedral : 21.988 165.317 1449 Min Nonbonded Distance : 1.747 Molprobity Statistics. All-atom Clashscore : 5.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.25 % Favored : 96.75 % Rotamer: Outliers : 1.68 % Allowed : 13.59 % Favored : 84.73 % 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: 1.14 (0.29), residues: 830 helix: 1.40 (0.21), residues: 583 sheet: -0.05 (0.77), residues: 45 loop : -0.82 (0.41), residues: 202 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 678 TYR 0.009 0.001 TYR A 697 PHE 0.005 0.001 PHE A 852 TRP 0.002 0.001 TRP A 773 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00296 ( 7460) covalent geometry : angle 0.53331 (10399) hydrogen bonds : bond 0.02612 ( 454) hydrogen bonds : angle 3.96411 ( 1284) metal coordination : bond 0.00129 ( 2) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 59 time to evaluate : 0.258 Fit side-chains REVERT: A 178 LEU cc_start: 0.8712 (tt) cc_final: 0.8289 (tt) REVERT: A 769 PRO cc_start: 0.7551 (Cg_endo) cc_final: 0.7295 (Cg_exo) REVERT: A 822 TYR cc_start: 0.7707 (t80) cc_final: 0.7469 (t80) outliers start: 11 outliers final: 10 residues processed: 67 average time/residue: 0.0677 time to fit residues: 6.8343 Evaluate side-chains 65 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 222 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 28 optimal weight: 0.0270 chunk 5 optimal weight: 2.9990 chunk 18 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 chunk 54 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 9.9990 chunk 12 optimal weight: 0.4980 chunk 43 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 253 HIS ** A 718 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4184 r_free = 0.4184 target = 0.194282 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4041 r_free = 0.4041 target = 0.177225 restraints weight = 7048.024| |-----------------------------------------------------------------------------| r_work (start): 0.4039 rms_B_bonded: 0.55 r_work: 0.3694 rms_B_bonded: 1.41 restraints_weight: 0.5000 r_work: 0.3510 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.3510 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7462 Z= 0.123 Angle : 0.532 8.628 10399 Z= 0.278 Chirality : 0.039 0.224 1256 Planarity : 0.005 0.050 1172 Dihedral : 21.873 164.766 1449 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 2.29 % Allowed : 12.82 % Favored : 84.89 % 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: 1.19 (0.29), residues: 830 helix: 1.43 (0.22), residues: 584 sheet: 0.08 (0.78), residues: 45 loop : -0.84 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 678 TYR 0.009 0.001 TYR A 697 PHE 0.005 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.007 0.000 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00273 ( 7460) covalent geometry : angle 0.53239 (10399) hydrogen bonds : bond 0.02421 ( 454) hydrogen bonds : angle 3.94266 ( 1284) metal coordination : bond 0.00102 ( 2) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 58 time to evaluate : 0.252 Fit side-chains REVERT: A 769 PRO cc_start: 0.7609 (Cg_endo) cc_final: 0.7352 (Cg_exo) REVERT: A 822 TYR cc_start: 0.7702 (t80) cc_final: 0.7462 (t80) outliers start: 15 outliers final: 9 residues processed: 67 average time/residue: 0.0619 time to fit residues: 6.2943 Evaluate side-chains 66 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.244 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 728 ASN Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 80 optimal weight: 9.9990 chunk 43 optimal weight: 0.5980 chunk 66 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 23 optimal weight: 0.7980 chunk 56 optimal weight: 1.9990 chunk 76 optimal weight: 0.7980 chunk 61 optimal weight: 0.8980 chunk 75 optimal weight: 6.9990 chunk 68 optimal weight: 0.0470 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 835 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4179 r_free = 0.4179 target = 0.193540 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 92)----------------| | r_work = 0.4020 r_free = 0.4020 target = 0.174842 restraints weight = 7038.434| |-----------------------------------------------------------------------------| r_work (start): 0.4018 rms_B_bonded: 0.57 r_work: 0.3574 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3430 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.3430 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7987 moved from start: 0.3905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 7462 Z= 0.128 Angle : 0.537 7.930 10399 Z= 0.280 Chirality : 0.039 0.193 1256 Planarity : 0.005 0.049 1172 Dihedral : 21.895 164.993 1449 Min Nonbonded Distance : 1.753 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 1.83 % Allowed : 13.44 % Favored : 84.73 % 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: 1.23 (0.29), residues: 830 helix: 1.44 (0.21), residues: 584 sheet: 0.22 (0.78), residues: 45 loop : -0.79 (0.41), residues: 201 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 414 TYR 0.009 0.001 TYR A 697 PHE 0.005 0.001 PHE A 852 TRP 0.002 0.001 TRP A 773 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00290 ( 7460) covalent geometry : angle 0.53706 (10399) hydrogen bonds : bond 0.02500 ( 454) hydrogen bonds : angle 3.91860 ( 1284) metal coordination : bond 0.00107 ( 2) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 56 time to evaluate : 0.244 Fit side-chains REVERT: A 769 PRO cc_start: 0.7589 (Cg_endo) cc_final: 0.7308 (Cg_exo) outliers start: 12 outliers final: 8 residues processed: 65 average time/residue: 0.0624 time to fit residues: 6.1968 Evaluate side-chains 63 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 55 time to evaluate : 0.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 23 optimal weight: 0.9980 chunk 33 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 85 optimal weight: 8.9990 chunk 3 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 5.9990 chunk 21 optimal weight: 0.7980 chunk 63 optimal weight: 0.9990 chunk 17 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 253 HIS A 835 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4161 r_free = 0.4161 target = 0.192058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.4028 r_free = 0.4028 target = 0.176306 restraints weight = 6916.072| |-----------------------------------------------------------------------------| r_work (start): 0.4028 rms_B_bonded: 0.54 r_work: 0.3651 rms_B_bonded: 1.55 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 2.72 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7462 Z= 0.149 Angle : 0.555 8.105 10399 Z= 0.289 Chirality : 0.040 0.161 1256 Planarity : 0.005 0.049 1172 Dihedral : 22.030 165.572 1449 Min Nonbonded Distance : 1.691 Molprobity Statistics. All-atom Clashscore : 6.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.53 % Allowed : 14.05 % Favored : 84.43 % 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: 1.21 (0.29), residues: 830 helix: 1.38 (0.21), residues: 585 sheet: 0.22 (0.78), residues: 45 loop : -0.65 (0.42), residues: 200 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 516 TYR 0.010 0.001 TYR A 697 PHE 0.004 0.001 PHE A 852 TRP 0.003 0.001 TRP A 773 HIS 0.007 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00347 ( 7460) covalent geometry : angle 0.55469 (10399) hydrogen bonds : bond 0.02812 ( 454) hydrogen bonds : angle 3.96495 ( 1284) metal coordination : bond 0.00170 ( 2) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.169 Fit side-chains REVERT: A 56 HIS cc_start: 0.7433 (OUTLIER) cc_final: 0.7201 (m-70) REVERT: A 769 PRO cc_start: 0.7705 (Cg_endo) cc_final: 0.7437 (Cg_exo) outliers start: 10 outliers final: 9 residues processed: 66 average time/residue: 0.0529 time to fit residues: 5.2582 Evaluate side-chains 67 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.146 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 HIS Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 85 optimal weight: 10.0000 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 3.9990 chunk 72 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 86 optimal weight: 5.9990 chunk 11 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 55 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 1.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 253 HIS A 835 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.189264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3969 r_free = 0.3969 target = 0.170656 restraints weight = 6987.232| |-----------------------------------------------------------------------------| r_work (start): 0.3967 rms_B_bonded: 0.58 r_work: 0.3506 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8065 moved from start: 0.4205 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 7462 Z= 0.219 Angle : 0.632 9.440 10399 Z= 0.331 Chirality : 0.042 0.128 1256 Planarity : 0.005 0.049 1172 Dihedral : 22.326 165.308 1449 Min Nonbonded Distance : 1.620 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 1.37 % Allowed : 14.35 % Favored : 84.27 % 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: 0.89 (0.29), residues: 830 helix: 1.13 (0.21), residues: 585 sheet: 0.06 (0.75), residues: 49 loop : -0.74 (0.43), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 516 TYR 0.011 0.001 TYR A 697 PHE 0.006 0.001 PHE A 52 TRP 0.003 0.001 TRP A 773 HIS 0.008 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00525 ( 7460) covalent geometry : angle 0.63199 (10399) hydrogen bonds : bond 0.03637 ( 454) hydrogen bonds : angle 4.10276 ( 1284) metal coordination : bond 0.00270 ( 2) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1660 Ramachandran restraints generated. 830 Oldfield, 0 Emsley, 830 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 57 time to evaluate : 0.246 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 64 average time/residue: 0.0599 time to fit residues: 5.7480 Evaluate side-chains 64 residues out of total 656 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 55 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 THR Chi-restraints excluded: chain A residue 245 LEU Chi-restraints excluded: chain A residue 607 ILE Chi-restraints excluded: chain A residue 622 VAL Chi-restraints excluded: chain A residue 656 VAL Chi-restraints excluded: chain A residue 709 ILE Chi-restraints excluded: chain A residue 755 VAL Chi-restraints excluded: chain A residue 756 VAL Chi-restraints excluded: chain A residue 861 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 87 random chunks: chunk 5 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 75 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 8 optimal weight: 1.9990 chunk 65 optimal weight: 2.9990 chunk 51 optimal weight: 0.9990 chunk 78 optimal weight: 6.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 HIS A 183 GLN A 253 HIS ** A 645 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 835 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.190842 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3987 r_free = 0.3987 target = 0.171965 restraints weight = 6977.366| |-----------------------------------------------------------------------------| r_work (start): 0.3985 rms_B_bonded: 0.60 r_work: 0.3531 rms_B_bonded: 2.49 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 moved from start: 0.4214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 7462 Z= 0.164 Angle : 0.577 8.523 10399 Z= 0.301 Chirality : 0.040 0.127 1256 Planarity : 0.005 0.050 1172 Dihedral : 22.165 165.387 1449 Min Nonbonded Distance : 1.687 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 1.68 % Allowed : 14.35 % Favored : 83.97 % 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: 0.98 (0.29), residues: 830 helix: 1.23 (0.21), residues: 586 sheet: -0.01 (0.74), residues: 49 loop : -0.77 (0.42), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 414 TYR 0.010 0.001 TYR A 697 PHE 0.004 0.001 PHE A 852 TRP 0.004 0.001 TRP A 773 HIS 0.008 0.001 HIS A 835 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 7460) covalent geometry : angle 0.57717 (10399) hydrogen bonds : bond 0.02979 ( 454) hydrogen bonds : angle 4.00190 ( 1284) metal coordination : bond 0.00136 ( 2) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1608.36 seconds wall clock time: 28 minutes 13.70 seconds (1693.70 seconds total)