Starting phenix.real_space_refine on Thu Jul 2 01:14:37 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8iva_35755/07_2026/8iva_35755.cif Found real_map, /net/cci-nas-00/data/ceres_data/8iva_35755/07_2026/8iva_35755.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8iva_35755/07_2026/8iva_35755.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8iva_35755/07_2026/8iva_35755.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8iva_35755/07_2026/8iva_35755.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8iva_35755/07_2026/8iva_35755.cif" model { file = "/net/cci-nas-00/data/ceres_data/8iva_35755/07_2026/8iva_35755.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8iva_35755/07_2026/8iva_35755.cif" } resolution = 3.95 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= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 26 5.16 5 C 3182 2.51 5 N 827 2.21 5 O 994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 5029 Number of models: 1 Model: "" Number of chains: 6 Chain: "C" Number of atoms: 929 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 929 Classifications: {'peptide': 122} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 118} Chain: "E" Number of atoms: 830 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 830 Classifications: {'peptide': 107} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 100} Chain: "G" Number of atoms: 1536 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1536 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 10, 'TRANS': 183} Chain: "L" Number of atoms: 788 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 788 Classifications: {'peptide': 104} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 2, 'TRANS': 100} Chain: "H" Number of atoms: 918 Number of conformers: 1 Conformer: "" Number of residues, atoms: 121, 918 Classifications: {'peptide': 121} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 117} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {'NAG': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 1.14, per 1000 atoms: 0.23 Number of scatterers: 5029 At special positions: 0 Unit cell: (80.912, 77.8, 108.142, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 26 16.00 O 994 8.00 N 827 7.00 C 3182 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS C 22 " - pdb=" SG CYS C 96 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 336 " - pdb=" SG CYS G 361 " distance=2.03 Simple disulfide: pdb=" SG CYS G 379 " - pdb=" SG CYS G 432 " distance=2.03 Simple disulfide: pdb=" SG CYS G 391 " - pdb=" SG CYS G 525 " distance=2.28 Simple disulfide: pdb=" SG CYS G 480 " - pdb=" SG CYS G 488 " distance=2.01 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 87 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " NAG-ASN " NAG A 1 " - " ASN G 343 " Time building additional restraints: 0.27 Conformation dependent library (CDL) restraints added in 133.6 milliseconds 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1176 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 15 sheets defined 5.6% alpha, 30.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.12 Creating SS restraints... Processing helix chain 'G' and resid 349 through 353 removed outlier: 3.529A pdb=" N ALA G 352 " --> pdb=" O SER G 349 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP G 353 " --> pdb=" O VAL G 350 " (cutoff:3.500A) No H-bonds generated for 'chain 'G' and resid 349 through 353' Processing helix chain 'G' and resid 364 through 370 removed outlier: 3.868A pdb=" N LEU G 368 " --> pdb=" O ASP G 364 " (cutoff:3.500A) Processing helix chain 'G' and resid 405 through 410 removed outlier: 4.130A pdb=" N ARG G 408 " --> pdb=" O ASP G 405 " (cutoff:3.500A) Processing helix chain 'G' and resid 416 through 422 Processing helix chain 'G' and resid 438 through 443 Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.695A pdb=" N THR H 31 " --> pdb=" O SER H 28 " (cutoff:3.500A) removed outlier: 3.566A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'H' and resid 28 through 32' Processing sheet with id=AA1, first strand: chain 'C' and resid 3 through 7 removed outlier: 3.669A pdb=" N GLN C 3 " --> pdb=" O SER C 25 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N SER C 25 " --> pdb=" O GLN C 3 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N SER C 21 " --> pdb=" O SER C 7 " (cutoff:3.500A) removed outlier: 3.583A pdb=" N THR C 78 " --> pdb=" O ASP C 73 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 10 through 12 removed outlier: 6.140A pdb=" N GLY C 10 " --> pdb=" O THR C 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 46 through 50 removed outlier: 4.834A pdb=" N TYR C 47 " --> pdb=" O ARG C 38 " (cutoff:3.500A) removed outlier: 5.853A pdb=" N ARG C 38 " --> pdb=" O TYR C 47 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N HIS C 35 " --> pdb=" O VAL C 97 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 5 through 7 removed outlier: 3.617A pdb=" N THR E 72 " --> pdb=" O SER E 65 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 10 through 11 removed outlier: 4.037A pdb=" N LEU E 11 " --> pdb=" O LYS E 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 44 through 46 Processing sheet with id=AA7, first strand: chain 'E' and resid 48 through 49 Processing sheet with id=AA8, first strand: chain 'G' and resid 354 through 358 removed outlier: 3.696A pdb=" N VAL G 395 " --> pdb=" O ILE G 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'G' and resid 452 through 454 Processing sheet with id=AB1, first strand: chain 'G' and resid 473 through 474 Processing sheet with id=AB2, first strand: chain 'L' and resid 19 through 29 removed outlier: 3.829A pdb=" N VAL L 25 " --> pdb=" O THR L 68 " (cutoff:3.500A) removed outlier: 6.196A pdb=" N THR L 68 " --> pdb=" O VAL L 25 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 52 through 53 removed outlier: 6.789A pdb=" N TRP L 34 " --> pdb=" O PHE L 46 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'H' and resid 3 through 7 removed outlier: 4.124A pdb=" N MET H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.920A pdb=" N SER H 25 " --> pdb=" O MET H 3 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N ASP H 73 " --> pdb=" O THR H 78 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N TYR H 80 " --> pdb=" O SER H 71 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.595A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N MET H 34 " --> pdb=" O ILE H 51 " (cutoff:3.500A) removed outlier: 6.139A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 5.249A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.731A pdb=" N THR H 40 " --> pdb=" O LEU H 45 " (cutoff:3.500A) removed outlier: 5.957A pdb=" N LEU H 45 " --> pdb=" O THR H 40 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.595A pdb=" N VAL H 12 " --> pdb=" O THR H 118 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) 127 hydrogen bonds defined for protein. 324 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.54 Time building geometry restraints manager: 0.37 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: 1558 1.34 - 1.46: 1395 1.46 - 1.58: 2165 1.58 - 1.71: 0 1.71 - 1.83: 36 Bond restraints: 5154 Sorted by residual: bond pdb=" CA ALA G 475 " pdb=" C ALA G 475 " ideal model delta sigma weight residual 1.522 1.571 -0.049 9.30e-03 1.16e+04 2.75e+01 bond pdb=" N ASP G 442 " pdb=" CA ASP G 442 " ideal model delta sigma weight residual 1.457 1.495 -0.037 1.16e-02 7.43e+03 1.04e+01 bond pdb=" N TYR G 473 " pdb=" CA TYR G 473 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.17e-02 7.31e+03 9.24e+00 bond pdb=" N GLN G 474 " pdb=" CA GLN G 474 " ideal model delta sigma weight residual 1.455 1.494 -0.039 1.29e-02 6.01e+03 9.15e+00 bond pdb=" N ALA G 475 " pdb=" CA ALA G 475 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.15e-02 7.56e+03 9.09e+00 ... (remaining 5149 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.00: 6902 3.00 - 5.99: 84 5.99 - 8.99: 11 8.99 - 11.99: 2 11.99 - 14.98: 2 Bond angle restraints: 7001 Sorted by residual: angle pdb=" C LEU G 335 " pdb=" N CYS G 336 " pdb=" CA CYS G 336 " ideal model delta sigma weight residual 120.49 135.47 -14.98 1.42e+00 4.96e-01 1.11e+02 angle pdb=" N ALA G 475 " pdb=" CA ALA G 475 " pdb=" C ALA G 475 " ideal model delta sigma weight residual 112.12 124.69 -12.57 1.34e+00 5.57e-01 8.80e+01 angle pdb=" N SER G 477 " pdb=" CA SER G 477 " pdb=" C SER G 477 " ideal model delta sigma weight residual 112.38 123.66 -11.28 1.22e+00 6.72e-01 8.55e+01 angle pdb=" N CYS G 480 " pdb=" CA CYS G 480 " pdb=" C CYS G 480 " ideal model delta sigma weight residual 112.45 121.62 -9.17 1.39e+00 5.18e-01 4.35e+01 angle pdb=" N LEU G 441 " pdb=" CA LEU G 441 " pdb=" C LEU G 441 " ideal model delta sigma weight residual 111.36 117.78 -6.42 1.09e+00 8.42e-01 3.47e+01 ... (remaining 6996 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 2698 17.75 - 35.50: 245 35.50 - 53.25: 46 53.25 - 71.00: 4 71.00 - 88.75: 5 Dihedral angle restraints: 2998 sinusoidal: 1137 harmonic: 1861 Sorted by residual: dihedral pdb=" CB CYS G 391 " pdb=" SG CYS G 391 " pdb=" SG CYS G 525 " pdb=" CB CYS G 525 " ideal model delta sinusoidal sigma weight residual 93.00 46.06 46.94 1 1.00e+01 1.00e-02 3.04e+01 dihedral pdb=" CA LEU G 461 " pdb=" C LEU G 461 " pdb=" N LYS G 462 " pdb=" CA LYS G 462 " ideal model delta harmonic sigma weight residual 180.00 157.06 22.94 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA TRP L 90 " pdb=" C TRP L 90 " pdb=" N SER L 91 " pdb=" CA SER L 91 " ideal model delta harmonic sigma weight residual -180.00 -159.93 -20.07 0 5.00e+00 4.00e-02 1.61e+01 ... (remaining 2995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.086: 654 0.086 - 0.172: 94 0.172 - 0.258: 10 0.258 - 0.343: 2 0.343 - 0.429: 3 Chirality restraints: 763 Sorted by residual: chirality pdb=" CA ALA G 475 " pdb=" N ALA G 475 " pdb=" C ALA G 475 " pdb=" CB ALA G 475 " both_signs ideal model delta sigma weight residual False 2.48 2.06 0.43 2.00e-01 2.50e+01 4.61e+00 chirality pdb=" CA CYS G 480 " pdb=" N CYS G 480 " pdb=" C CYS G 480 " pdb=" CB CYS G 480 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 4.02e+00 chirality pdb=" CA SER G 477 " pdb=" N SER G 477 " pdb=" C SER G 477 " pdb=" CB SER G 477 " both_signs ideal model delta sigma weight residual False 2.51 2.11 0.40 2.00e-01 2.50e+01 3.91e+00 ... (remaining 760 not shown) Planarity restraints: 892 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C TYR E 94 " 0.047 5.00e-02 4.00e+02 7.12e-02 8.11e+00 pdb=" N PRO E 95 " -0.123 5.00e-02 4.00e+02 pdb=" CA PRO E 95 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO E 95 " 0.040 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE G 472 " -0.014 2.00e-02 2.50e+03 2.81e-02 7.89e+00 pdb=" C ILE G 472 " 0.049 2.00e-02 2.50e+03 pdb=" O ILE G 472 " -0.018 2.00e-02 2.50e+03 pdb=" N TYR G 473 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR H 40 " -0.043 5.00e-02 4.00e+02 6.43e-02 6.62e+00 pdb=" N PRO H 41 " 0.111 5.00e-02 4.00e+02 pdb=" CA PRO H 41 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO H 41 " -0.036 5.00e-02 4.00e+02 ... (remaining 889 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1604 2.82 - 3.34: 4003 3.34 - 3.86: 8000 3.86 - 4.38: 8740 4.38 - 4.90: 15568 Nonbonded interactions: 37915 Sorted by model distance: nonbonded pdb=" O TYR E 49 " pdb=" OG SER E 53 " model vdw 2.302 3.040 nonbonded pdb=" O VAL L 29 " pdb=" OH TYR L 70 " model vdw 2.324 3.040 nonbonded pdb=" OH TYR L 86 " pdb=" O LYS H 43 " model vdw 2.349 3.040 nonbonded pdb=" OH TYR H 59 " pdb=" OH TYR H 103 " model vdw 2.355 3.040 nonbonded pdb=" NE2 GLN E 6 " pdb=" OG1 THR E 102 " model vdw 2.378 3.120 ... (remaining 37910 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 15.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.090 Check model and map are aligned: 0.010 Set scattering table: 0.020 Process input model: 5.070 Find NCS groups from input model: 0.020 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:1.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6999 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 : 0.007 0.250 5164 Z= 0.346 Angle : 1.024 24.285 7023 Z= 0.618 Chirality : 0.066 0.429 763 Planarity : 0.007 0.071 891 Dihedral : 13.878 88.750 1798 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 5.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.37 % Favored : 92.63 % Rotamer: Outliers : 0.54 % Allowed : 7.43 % Favored : 92.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -4.03 (0.28), residues: 638 helix: -5.15 (0.31), residues: 14 sheet: -2.71 (0.30), residues: 223 loop : -2.65 (0.26), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 457 TYR 0.027 0.002 TYR E 94 PHE 0.022 0.002 PHE E 83 TRP 0.023 0.002 TRP C 106 HIS 0.004 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00552 / 0.30 ( 5154) covalent geometry : angle 0.97365 / 0.60 ( 7001) SS BOND : bond 0.08879 / 7.38 ( 8) SS BOND : angle 6.36753 / 3.75 ( 16) hydrogen bonds : bond 0.27035 / 18.65 ( 123) hydrogen bonds : angle 11.18507 / 7.21 ( 324) link_BETA1-4 : bond 0.00671 / 0.35 ( 1) link_BETA1-4 : angle 1.30442 / 0.76 ( 3) link_NAG-ASN : bond 0.00196 / 0.10 ( 1) link_NAG-ASN : angle 5.17553 / 2.69 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 201 time to evaluate : 0.179 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 19 ARG cc_start: 0.8186 (ttm170) cc_final: 0.7986 (ptm-80) REVERT: C 59 TYR cc_start: 0.8333 (t80) cc_final: 0.8079 (t80) REVERT: C 97 VAL cc_start: 0.8206 (m) cc_final: 0.7978 (m) REVERT: E 23 CYS cc_start: 0.7962 (t) cc_final: 0.7397 (t) REVERT: E 24 ARG cc_start: 0.7893 (ttp-110) cc_final: 0.7403 (ttm110) REVERT: E 27 GLN cc_start: 0.8312 (tt0) cc_final: 0.7881 (mp10) REVERT: E 42 LYS cc_start: 0.8276 (pttm) cc_final: 0.7935 (mtpt) REVERT: E 61 ARG cc_start: 0.7920 (ptt-90) cc_final: 0.7318 (ptt90) REVERT: E 82 ASP cc_start: 0.8556 (m-30) cc_final: 0.7458 (m-30) REVERT: E 89 GLN cc_start: 0.8162 (tm-30) cc_final: 0.7480 (tm-30) REVERT: E 90 GLN cc_start: 0.7557 (pp30) cc_final: 0.6810 (pp30) REVERT: E 93 SER cc_start: 0.8477 (m) cc_final: 0.8136 (m) REVERT: E 107 LYS cc_start: 0.4448 (tttt) cc_final: 0.3687 (tptm) REVERT: G 335 LEU cc_start: 0.8075 (mp) cc_final: 0.7866 (mt) REVERT: G 369 TYR cc_start: 0.9026 (t80) cc_final: 0.8627 (t80) REVERT: G 378 LYS cc_start: 0.6890 (mttm) cc_final: 0.6514 (mtmm) REVERT: G 442 ASP cc_start: 0.8631 (m-30) cc_final: 0.8398 (m-30) REVERT: G 465 GLU cc_start: 0.8580 (tt0) cc_final: 0.8214 (tt0) REVERT: G 471 GLU cc_start: 0.8086 (tt0) cc_final: 0.7696 (pt0) REVERT: L 1 GLN cc_start: 0.8967 (pt0) cc_final: 0.8651 (pp30) REVERT: L 31 ASP cc_start: 0.7177 (p0) cc_final: 0.6598 (p0) REVERT: L 32 MET cc_start: 0.8278 (tpp) cc_final: 0.7995 (mmm) REVERT: L 34 TRP cc_start: 0.8514 (m100) cc_final: 0.7779 (m100) REVERT: L 44 LYS cc_start: 0.7328 (mtmm) cc_final: 0.6966 (ttpt) REVERT: L 86 TYR cc_start: 0.8370 (m-80) cc_final: 0.7988 (m-10) REVERT: H 19 LYS cc_start: 0.8173 (tttt) cc_final: 0.7585 (ptmt) REVERT: H 73 ASP cc_start: 0.7287 (t0) cc_final: 0.6969 (t0) REVERT: H 76 MET cc_start: 0.7944 (mpp) cc_final: 0.7696 (mtm) REVERT: H 93 MET cc_start: 0.6600 (tpp) cc_final: 0.6290 (tpp) REVERT: H 102 ASN cc_start: 0.8301 (p0) cc_final: 0.8001 (p0) REVERT: H 107 VAL cc_start: 0.8477 (p) cc_final: 0.8157 (t) outliers start: 3 outliers final: 0 residues processed: 204 average time/residue: 0.0702 time to fit residues: 17.8116 Evaluate side-chains 159 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 159 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 48 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 61 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 chunk 25 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 82 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3402 r_free = 0.3402 target = 0.112130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.094592 restraints weight = 10485.008| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.097645 restraints weight = 6109.940| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.099775 restraints weight = 4233.767| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.101219 restraints weight = 3258.548| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3259 r_free = 0.3259 target = 0.102307 restraints weight = 2695.468| |-----------------------------------------------------------------------------| r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3217 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3217 r_free = 0.3217 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3216 r_free = 0.3216 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 6 (11 function evaluations) r_final: 0.3216 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.2096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 5164 Z= 0.168 Angle : 0.670 7.996 7023 Z= 0.358 Chirality : 0.046 0.169 763 Planarity : 0.005 0.057 891 Dihedral : 6.072 74.475 712 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.96 % Favored : 94.04 % Rotamer: Outliers : 4.89 % Allowed : 15.76 % Favored : 79.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -3.39 (0.29), residues: 638 helix: -3.43 (0.83), residues: 21 sheet: -1.92 (0.33), residues: 222 loop : -2.47 (0.27), residues: 395 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 408 TYR 0.025 0.002 TYR E 94 PHE 0.022 0.002 PHE G 400 TRP 0.018 0.002 TRP C 106 HIS 0.003 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00385 / 0.17 ( 5154) covalent geometry : angle 0.65848 / 0.35 ( 7001) SS BOND : bond 0.00675 / 0.49 ( 8) SS BOND : angle 2.29138 / 1.25 ( 16) hydrogen bonds : bond 0.04432 / 3.15 ( 123) hydrogen bonds : angle 7.64872 / 5.13 ( 324) link_BETA1-4 : bond 0.00264 / 0.14 ( 1) link_BETA1-4 : angle 0.93964 / 0.52 ( 3) link_NAG-ASN : bond 0.00073 / 0.04 ( 1) link_NAG-ASN : angle 3.32290 / 1.75 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 163 time to evaluate : 0.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ARG cc_start: 0.8668 (ptm160) cc_final: 0.8453 (ptm160) REVERT: C 76 LYS cc_start: 0.8728 (mmtm) cc_final: 0.8440 (mmtm) REVERT: E 89 GLN cc_start: 0.9219 (tm-30) cc_final: 0.8660 (tm-30) REVERT: E 107 LYS cc_start: 0.5172 (tttt) cc_final: 0.4681 (tptm) REVERT: G 378 LYS cc_start: 0.8842 (mttm) cc_final: 0.8349 (mtmm) REVERT: L 34 TRP cc_start: 0.8736 (m100) cc_final: 0.8272 (m100) REVERT: L 44 LYS cc_start: 0.8366 (mtmm) cc_final: 0.8135 (ttpt) REVERT: H 76 MET cc_start: 0.8173 (mpp) cc_final: 0.7743 (mtm) REVERT: H 93 MET cc_start: 0.7494 (tpp) cc_final: 0.7273 (tpp) outliers start: 27 outliers final: 14 residues processed: 176 average time/residue: 0.0746 time to fit residues: 16.5383 Evaluate side-chains 152 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 138 time to evaluate : 0.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain H residue 25 SER Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 19 optimal weight: 4.9990 chunk 55 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 54 optimal weight: 0.9990 chunk 14 optimal weight: 1.9990 chunk 56 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 47 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 overall best weight: 1.3788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... C 102 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107786 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.090462 restraints weight = 10606.958| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3120 r_free = 0.3120 target = 0.093488 restraints weight = 6067.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.095592 restraints weight = 4161.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.097071 restraints weight = 3170.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3192 r_free = 0.3192 target = 0.098062 restraints weight = 2595.759| |-----------------------------------------------------------------------------| r_work (final): 0.3182 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3175 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3175 r_free = 0.3175 target_work(ls_wunit_k1) = 0.097 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (16 function evaluations) r_final: 0.3175 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2770 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 5164 Z= 0.230 Angle : 0.713 9.066 7023 Z= 0.378 Chirality : 0.048 0.175 763 Planarity : 0.005 0.056 891 Dihedral : 6.155 77.256 712 Min Nonbonded Distance : 2.569 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.84 % Favored : 92.16 % Rotamer: Outliers : 4.53 % Allowed : 19.93 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -3.18 (0.30), residues: 638 helix: -3.20 (0.89), residues: 21 sheet: -1.75 (0.34), residues: 219 loop : -2.35 (0.27), residues: 398 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG G 408 TYR 0.021 0.002 TYR E 94 PHE 0.024 0.002 PHE G 347 TRP 0.017 0.002 TRP C 106 HIS 0.002 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00536 / 0.23 ( 5154) covalent geometry : angle 0.70489 / 0.38 ( 7001) SS BOND : bond 0.00640 / 0.42 ( 8) SS BOND : angle 1.91070 / 1.02 ( 16) hydrogen bonds : bond 0.04299 / 3.10 ( 123) hydrogen bonds : angle 7.11163 / 4.85 ( 324) link_BETA1-4 : bond 0.00022 / 0.01 ( 1) link_BETA1-4 : angle 0.97151 / 0.54 ( 3) link_NAG-ASN : bond 0.00213 / 0.11 ( 1) link_NAG-ASN : angle 3.26087 / 1.71 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 137 time to evaluate : 0.115 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 76 LYS cc_start: 0.8806 (mmtm) cc_final: 0.8540 (mmtm) REVERT: C 83 MET cc_start: 0.7832 (mtt) cc_final: 0.7539 (mtt) REVERT: C 87 ARG cc_start: 0.7943 (mtp-110) cc_final: 0.7547 (mtp-110) REVERT: C 89 GLU cc_start: 0.7771 (mp0) cc_final: 0.7330 (mp0) REVERT: E 89 GLN cc_start: 0.9248 (tm-30) cc_final: 0.8694 (tm-30) REVERT: G 378 LYS cc_start: 0.8902 (mttm) cc_final: 0.8345 (mtmm) REVERT: G 462 LYS cc_start: 0.9038 (pttt) cc_final: 0.8686 (pttm) REVERT: G 465 GLU cc_start: 0.8547 (tt0) cc_final: 0.8261 (tt0) REVERT: H 73 ASP cc_start: 0.7365 (t0) cc_final: 0.6201 (t0) REVERT: H 76 MET cc_start: 0.8289 (mpp) cc_final: 0.7966 (mpp) REVERT: H 95 TYR cc_start: 0.9034 (m-10) cc_final: 0.8827 (m-10) outliers start: 25 outliers final: 18 residues processed: 153 average time/residue: 0.0659 time to fit residues: 12.8054 Evaluate side-chains 146 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 128 time to evaluate : 0.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 5 VAL Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 1 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 50 optimal weight: 1.9990 chunk 4 optimal weight: 0.6980 chunk 61 optimal weight: 0.9980 chunk 57 optimal weight: 0.6980 chunk 55 optimal weight: 0.8980 chunk 35 optimal weight: 0.0170 chunk 21 optimal weight: 1.9990 overall best weight: 0.6418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109869 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.092375 restraints weight = 10497.134| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095489 restraints weight = 5946.050| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3187 r_free = 0.3187 target = 0.097640 restraints weight = 4061.745| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.099129 restraints weight = 3092.822| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100161 restraints weight = 2523.805| |-----------------------------------------------------------------------------| r_work (final): 0.3223 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3240 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3240 r_free = 0.3240 target_work(ls_wunit_k1) = 0.101 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3240 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.3090 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5164 Z= 0.132 Angle : 0.630 8.337 7023 Z= 0.333 Chirality : 0.045 0.159 763 Planarity : 0.005 0.052 891 Dihedral : 5.753 75.993 712 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 4.71 % Allowed : 21.56 % Favored : 73.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.91 (0.31), residues: 638 helix: -3.65 (0.74), residues: 27 sheet: -1.46 (0.35), residues: 226 loop : -2.16 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.019 0.002 TYR C 95 PHE 0.014 0.002 PHE C 27 TRP 0.015 0.001 TRP C 106 HIS 0.002 0.001 HIS C 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00311 / 0.13 ( 5154) covalent geometry : angle 0.62097 / 0.33 ( 7001) SS BOND : bond 0.00516 / 0.35 ( 8) SS BOND : angle 1.98278 / 1.11 ( 16) hydrogen bonds : bond 0.03644 / 2.63 ( 123) hydrogen bonds : angle 6.60507 / 4.51 ( 324) link_BETA1-4 : bond 0.00349 / 0.18 ( 1) link_BETA1-4 : angle 0.88166 / 0.51 ( 3) link_NAG-ASN : bond 0.00045 / 0.02 ( 1) link_NAG-ASN : angle 2.88767 / 1.52 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 170 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 144 time to evaluate : 0.184 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9315 (mmmt) cc_final: 0.9082 (mmtm) REVERT: C 76 LYS cc_start: 0.8816 (mmtm) cc_final: 0.8597 (mmtm) REVERT: C 87 ARG cc_start: 0.7925 (mtp-110) cc_final: 0.7511 (mtp-110) REVERT: C 89 GLU cc_start: 0.7664 (mp0) cc_final: 0.7223 (mp0) REVERT: G 378 LYS cc_start: 0.8898 (mttm) cc_final: 0.8297 (mtmm) REVERT: G 462 LYS cc_start: 0.9057 (pttt) cc_final: 0.8618 (pttm) REVERT: L 2 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8814 (mt) REVERT: H 73 ASP cc_start: 0.7267 (t0) cc_final: 0.6101 (t0) REVERT: H 76 MET cc_start: 0.8259 (mpp) cc_final: 0.7964 (mpp) outliers start: 26 outliers final: 20 residues processed: 158 average time/residue: 0.0701 time to fit residues: 13.9815 Evaluate side-chains 152 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 54 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 5.9990 chunk 52 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 0.9990 chunk 51 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... E 89 GLN ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.103374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2987 r_free = 0.2987 target = 0.085438 restraints weight = 10906.419| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.088421 restraints weight = 6298.015| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.090466 restraints weight = 4349.029| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.091910 restraints weight = 3357.924| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3113 r_free = 0.3113 target = 0.092962 restraints weight = 2781.947| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3152 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3152 r_free = 0.3152 target_work(ls_wunit_k1) = 0.095 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3152 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.3402 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.088 5164 Z= 0.317 Angle : 0.783 9.449 7023 Z= 0.412 Chirality : 0.049 0.197 763 Planarity : 0.005 0.058 891 Dihedral : 6.332 81.593 712 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.40 % Favored : 90.60 % Rotamer: Outliers : 5.62 % Allowed : 22.28 % Favored : 72.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -3.07 (0.30), residues: 638 helix: -3.65 (0.72), residues: 27 sheet: -1.62 (0.34), residues: 226 loop : -2.23 (0.28), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 509 TYR 0.022 0.002 TYR E 94 PHE 0.021 0.002 PHE E 91 TRP 0.016 0.002 TRP C 106 HIS 0.004 0.002 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00733 / 0.32 ( 5154) covalent geometry : angle 0.76930 / 0.41 ( 7001) SS BOND : bond 0.00559 / 0.33 ( 8) SS BOND : angle 2.74873 / 1.38 ( 16) hydrogen bonds : bond 0.04416 / 3.19 ( 123) hydrogen bonds : angle 6.91226 / 4.74 ( 324) link_BETA1-4 : bond 0.00275 / 0.14 ( 1) link_BETA1-4 : angle 1.22335 / 0.66 ( 3) link_NAG-ASN : bond 0.00421 / 0.22 ( 1) link_NAG-ASN : angle 3.25045 / 1.70 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 126 time to evaluate : 0.201 Fit side-chains revert: symmetry clash REVERT: C 73 ASP cc_start: 0.8576 (t70) cc_final: 0.7447 (t70) REVERT: C 76 LYS cc_start: 0.8831 (mmtm) cc_final: 0.8522 (mmtm) REVERT: C 87 ARG cc_start: 0.7989 (mtp-110) cc_final: 0.7493 (mtp-110) REVERT: C 89 GLU cc_start: 0.7837 (mp0) cc_final: 0.7273 (mp0) REVERT: E 89 GLN cc_start: 0.9270 (OUTLIER) cc_final: 0.8875 (pp30) REVERT: G 353 TRP cc_start: 0.8927 (p-90) cc_final: 0.8694 (p-90) REVERT: G 378 LYS cc_start: 0.8896 (mttm) cc_final: 0.8322 (mtmm) REVERT: L 2 ILE cc_start: 0.9139 (OUTLIER) cc_final: 0.8779 (mt) REVERT: H 73 ASP cc_start: 0.7422 (t0) cc_final: 0.6568 (t0) REVERT: H 76 MET cc_start: 0.8398 (mpp) cc_final: 0.8173 (mpp) outliers start: 31 outliers final: 25 residues processed: 148 average time/residue: 0.0616 time to fit residues: 11.8756 Evaluate side-chains 149 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 122 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 89 GLN Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 107 VAL Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 10 optimal weight: 0.7980 chunk 49 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 0.5980 chunk 32 optimal weight: 0.9980 chunk 37 optimal weight: 0.8980 chunk 61 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 89 GLN E 90 GLN ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.109520 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.092287 restraints weight = 10605.430| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3150 r_free = 0.3150 target = 0.095289 restraints weight = 5994.615| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097397 restraints weight = 4110.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3207 r_free = 0.3207 target = 0.098850 restraints weight = 3132.031| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.099855 restraints weight = 2565.238| |-----------------------------------------------------------------------------| r_work (final): 0.3197 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3221 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3221 r_free = 0.3221 target_work(ls_wunit_k1) = 0.100 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3221 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8391 moved from start: 0.3498 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 5164 Z= 0.147 Angle : 0.659 8.522 7023 Z= 0.348 Chirality : 0.045 0.164 763 Planarity : 0.004 0.053 891 Dihedral : 6.010 81.052 712 Min Nonbonded Distance : 2.357 Molprobity Statistics. All-atom Clashscore : 9.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.49 % Favored : 94.51 % Rotamer: Outliers : 5.62 % Allowed : 23.91 % Favored : 70.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.88 (0.31), residues: 638 helix: -3.60 (0.75), residues: 27 sheet: -1.45 (0.34), residues: 228 loop : -2.12 (0.28), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG E 18 TYR 0.020 0.002 TYR E 94 PHE 0.014 0.002 PHE G 377 TRP 0.016 0.002 TRP C 106 HIS 0.003 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00345 / 0.15 ( 5154) covalent geometry : angle 0.64939 / 0.34 ( 7001) SS BOND : bond 0.00696 / 0.49 ( 8) SS BOND : angle 2.14558 / 1.18 ( 16) hydrogen bonds : bond 0.03610 / 2.62 ( 123) hydrogen bonds : angle 6.61655 / 4.53 ( 324) link_BETA1-4 : bond 0.00245 / 0.13 ( 1) link_BETA1-4 : angle 0.85084 / 0.49 ( 3) link_NAG-ASN : bond 0.00072 / 0.04 ( 1) link_NAG-ASN : angle 2.90536 / 1.54 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 0.174 Fit side-chains REVERT: C 43 LYS cc_start: 0.9236 (mmmt) cc_final: 0.8943 (mmtm) REVERT: C 73 ASP cc_start: 0.8563 (t70) cc_final: 0.7105 (t70) REVERT: C 76 LYS cc_start: 0.8782 (mmtm) cc_final: 0.8454 (mmtm) REVERT: C 87 ARG cc_start: 0.7920 (mtp-110) cc_final: 0.7446 (mtp-110) REVERT: C 89 GLU cc_start: 0.7695 (mp0) cc_final: 0.7203 (mp0) REVERT: C 98 LYS cc_start: 0.8915 (tmmt) cc_final: 0.8493 (tttm) REVERT: E 90 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8825 (pp30) REVERT: G 353 TRP cc_start: 0.8830 (p-90) cc_final: 0.8572 (p-90) REVERT: G 378 LYS cc_start: 0.8923 (mttm) cc_final: 0.8331 (mtmm) REVERT: L 2 ILE cc_start: 0.9056 (OUTLIER) cc_final: 0.8829 (mt) REVERT: H 73 ASP cc_start: 0.7299 (t0) cc_final: 0.6467 (t0) REVERT: H 76 MET cc_start: 0.8351 (mpp) cc_final: 0.8145 (mpp) REVERT: H 87 ARG cc_start: 0.7946 (mtt180) cc_final: 0.7429 (mtt180) outliers start: 31 outliers final: 25 residues processed: 159 average time/residue: 0.0615 time to fit residues: 12.6465 Evaluate side-chains 157 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 130 time to evaluate : 0.135 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 90 GLN Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 57 VAL Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 46 optimal weight: 0.0870 chunk 18 optimal weight: 4.9990 chunk 19 optimal weight: 0.8980 chunk 2 optimal weight: 0.0570 chunk 8 optimal weight: 0.1980 chunk 39 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 overall best weight: 0.4076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3369 r_free = 0.3369 target = 0.109737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.092364 restraints weight = 10320.012| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.095442 restraints weight = 5856.834| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3184 r_free = 0.3184 target = 0.097563 restraints weight = 3985.990| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.099053 restraints weight = 3034.939| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.100124 restraints weight = 2473.628| |-----------------------------------------------------------------------------| r_work (final): 0.3252 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3254 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3254 r_free = 0.3254 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3254 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8348 moved from start: 0.3623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5164 Z= 0.118 Angle : 0.650 8.791 7023 Z= 0.338 Chirality : 0.045 0.158 763 Planarity : 0.004 0.053 891 Dihedral : 5.737 77.302 712 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Rotamer: Outliers : 4.89 % Allowed : 25.36 % Favored : 69.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.63 (0.31), residues: 638 helix: -3.50 (0.78), residues: 27 sheet: -1.20 (0.34), residues: 232 loop : -2.01 (0.29), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.016 0.001 TYR E 94 PHE 0.020 0.002 PHE L 46 TRP 0.013 0.001 TRP C 106 HIS 0.003 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00271 / 0.12 ( 5154) covalent geometry : angle 0.63910 / 0.33 ( 7001) SS BOND : bond 0.00412 / 0.22 ( 8) SS BOND : angle 2.24304 / 1.11 ( 16) hydrogen bonds : bond 0.03319 / 2.39 ( 123) hydrogen bonds : angle 6.50957 / 4.44 ( 324) link_BETA1-4 : bond 0.00344 / 0.18 ( 1) link_BETA1-4 : angle 0.82452 / 0.47 ( 3) link_NAG-ASN : bond 0.00032 / 0.02 ( 1) link_NAG-ASN : angle 2.82207 / 1.50 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.179 Fit side-chains revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9226 (mmmt) cc_final: 0.9003 (mmtm) REVERT: C 73 ASP cc_start: 0.8605 (t70) cc_final: 0.7762 (t70) REVERT: C 83 MET cc_start: 0.7529 (mtt) cc_final: 0.7048 (mtt) REVERT: C 87 ARG cc_start: 0.7814 (mtp-110) cc_final: 0.7349 (mtp-110) REVERT: C 89 GLU cc_start: 0.7735 (mp0) cc_final: 0.7314 (mp0) REVERT: G 353 TRP cc_start: 0.8788 (p-90) cc_final: 0.8534 (p-90) REVERT: G 462 LYS cc_start: 0.8899 (pttt) cc_final: 0.8657 (pttm) REVERT: L 2 ILE cc_start: 0.9033 (OUTLIER) cc_final: 0.8696 (mt) REVERT: H 73 ASP cc_start: 0.7225 (t0) cc_final: 0.5938 (t0) REVERT: H 76 MET cc_start: 0.8318 (mpp) cc_final: 0.7941 (mpp) REVERT: H 87 ARG cc_start: 0.7939 (mtt180) cc_final: 0.7427 (mtt180) outliers start: 27 outliers final: 24 residues processed: 151 average time/residue: 0.0565 time to fit residues: 11.2552 Evaluate side-chains 154 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 129 time to evaluate : 0.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 47 LEU Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 25 VAL Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 20 optimal weight: 0.2980 chunk 40 optimal weight: 2.9990 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 12 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 49 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 overall best weight: 1.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 88 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.102536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.2968 r_free = 0.2968 target = 0.084838 restraints weight = 10703.652| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3015 r_free = 0.3015 target = 0.087634 restraints weight = 6357.608| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.089603 restraints weight = 4484.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3068 r_free = 0.3068 target = 0.090892 restraints weight = 3508.954| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3085 r_free = 0.3085 target = 0.091904 restraints weight = 2954.595| |-----------------------------------------------------------------------------| r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8443 moved from start: 0.3720 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.066 5164 Z= 0.240 Angle : 0.725 9.035 7023 Z= 0.381 Chirality : 0.046 0.177 763 Planarity : 0.005 0.055 891 Dihedral : 6.053 79.673 712 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.15 % Favored : 91.85 % Rotamer: Outliers : 5.80 % Allowed : 26.63 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.65 (0.31), residues: 638 helix: -3.60 (0.75), residues: 27 sheet: -1.23 (0.34), residues: 224 loop : -2.01 (0.29), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 457 TYR 0.022 0.002 TYR C 95 PHE 0.015 0.002 PHE E 91 TRP 0.014 0.002 TRP C 106 HIS 0.003 0.001 HIS L 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00562 / 0.24 ( 5154) covalent geometry : angle 0.71380 / 0.38 ( 7001) SS BOND : bond 0.00578 / 0.40 ( 8) SS BOND : angle 2.47583 / 1.33 ( 16) hydrogen bonds : bond 0.03876 / 2.81 ( 123) hydrogen bonds : angle 6.68122 / 4.54 ( 324) link_BETA1-4 : bond 0.00372 / 0.20 ( 1) link_BETA1-4 : angle 0.97150 / 0.53 ( 3) link_NAG-ASN : bond 0.00405 / 0.21 ( 1) link_NAG-ASN : angle 2.97805 / 1.58 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.189 Fit side-chains revert: symmetry clash REVERT: C 73 ASP cc_start: 0.8702 (t70) cc_final: 0.7725 (t0) REVERT: C 83 MET cc_start: 0.7603 (mtt) cc_final: 0.7296 (mtt) REVERT: C 87 ARG cc_start: 0.7896 (mtp-110) cc_final: 0.7450 (mtp-110) REVERT: C 89 GLU cc_start: 0.7716 (mp0) cc_final: 0.7247 (mp0) REVERT: G 353 TRP cc_start: 0.8898 (p-90) cc_final: 0.8661 (p-90) REVERT: G 378 LYS cc_start: 0.8952 (mttm) cc_final: 0.8394 (mtmm) REVERT: L 2 ILE cc_start: 0.9076 (OUTLIER) cc_final: 0.8862 (mt) REVERT: L 90 TRP cc_start: 0.9065 (t60) cc_final: 0.8513 (t60) REVERT: H 73 ASP cc_start: 0.7316 (t0) cc_final: 0.6594 (t0) outliers start: 32 outliers final: 27 residues processed: 151 average time/residue: 0.0690 time to fit residues: 13.5969 Evaluate side-chains 154 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 126 time to evaluate : 0.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 64 VAL Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 82 ASP Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain H residue 12 VAL Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 0 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 15 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 6 optimal weight: 0.9990 chunk 59 optimal weight: 2.9990 chunk 43 optimal weight: 2.9990 chunk 39 optimal weight: 0.5980 chunk 54 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 88 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3339 r_free = 0.3339 target = 0.107759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.090389 restraints weight = 10584.619| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.093409 restraints weight = 6018.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.095515 restraints weight = 4110.045| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.096964 restraints weight = 3140.790| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.097978 restraints weight = 2575.144| |-----------------------------------------------------------------------------| r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3108 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3108 r_free = 0.3108 target_work(ls_wunit_k1) = 0.094 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3108 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 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 : 0.004 0.049 5164 Z= 0.174 Angle : 0.699 8.880 7023 Z= 0.365 Chirality : 0.046 0.165 763 Planarity : 0.004 0.054 891 Dihedral : 6.018 79.827 712 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.05 % Favored : 92.95 % Rotamer: Outliers : 4.89 % Allowed : 27.36 % Favored : 67.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.60 (0.31), residues: 638 helix: -3.45 (0.79), residues: 27 sheet: -1.21 (0.35), residues: 225 loop : -1.96 (0.29), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.020 0.002 TYR E 94 PHE 0.014 0.002 PHE L 46 TRP 0.015 0.002 TRP C 106 HIS 0.002 0.001 HIS L 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00413 / 0.17 ( 5154) covalent geometry : angle 0.68905 / 0.36 ( 7001) SS BOND : bond 0.00617 / 0.44 ( 8) SS BOND : angle 2.30028 / 1.23 ( 16) hydrogen bonds : bond 0.03550 / 2.57 ( 123) hydrogen bonds : angle 6.57773 / 4.46 ( 324) link_BETA1-4 : bond 0.00153 / 0.08 ( 1) link_BETA1-4 : angle 0.93880 / 0.53 ( 3) link_NAG-ASN : bond 0.00197 / 0.10 ( 1) link_NAG-ASN : angle 2.87276 / 1.53 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9271 (mmmt) cc_final: 0.8932 (mmtm) REVERT: C 73 ASP cc_start: 0.8609 (t70) cc_final: 0.7635 (t0) REVERT: C 83 MET cc_start: 0.7679 (mtt) cc_final: 0.7374 (mtt) REVERT: C 87 ARG cc_start: 0.7926 (mtp-110) cc_final: 0.7443 (mtp-110) REVERT: C 89 GLU cc_start: 0.7722 (mp0) cc_final: 0.7205 (mp0) REVERT: G 353 TRP cc_start: 0.8865 (p-90) cc_final: 0.8618 (p-90) REVERT: G 378 LYS cc_start: 0.8891 (mttm) cc_final: 0.8266 (mtmm) REVERT: L 2 ILE cc_start: 0.9081 (OUTLIER) cc_final: 0.8864 (mt) REVERT: H 73 ASP cc_start: 0.7270 (t0) cc_final: 0.6569 (t0) REVERT: H 76 MET cc_start: 0.8283 (mpp) cc_final: 0.7819 (mpp) REVERT: H 106 SER cc_start: 0.9024 (t) cc_final: 0.8818 (t) outliers start: 27 outliers final: 24 residues processed: 145 average time/residue: 0.0621 time to fit residues: 11.7991 Evaluate side-chains 155 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 130 time to evaluate : 0.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain G residue 524 VAL Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 45 optimal weight: 2.9990 chunk 44 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 48 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 chunk 27 optimal weight: 0.2980 chunk 53 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** C 99 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.107656 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3060 r_free = 0.3060 target = 0.089872 restraints weight = 10596.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.092885 restraints weight = 6080.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3144 r_free = 0.3144 target = 0.094976 restraints weight = 4199.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.096407 restraints weight = 3235.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.097386 restraints weight = 2674.481| |-----------------------------------------------------------------------------| r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3100 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3100 r_free = 0.3100 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3100 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8393 moved from start: 0.3940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5164 Z= 0.178 Angle : 0.720 8.868 7023 Z= 0.377 Chirality : 0.046 0.165 763 Planarity : 0.005 0.054 891 Dihedral : 6.052 79.663 712 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 10.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 4.89 % Allowed : 27.54 % Favored : 67.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.57 (0.31), residues: 638 helix: -3.41 (0.82), residues: 27 sheet: -1.19 (0.35), residues: 223 loop : -1.94 (0.29), residues: 388 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.021 0.002 TYR C 95 PHE 0.014 0.002 PHE G 347 TRP 0.014 0.001 TRP C 106 HIS 0.004 0.001 HIS L 88 Details of bonding type rmsd/Z covalent geometry : bond 0.00421 / 0.18 ( 5154) covalent geometry : angle 0.71323 / 0.37 ( 7001) SS BOND : bond 0.00636 / 0.46 ( 8) SS BOND : angle 1.86795 / 0.93 ( 16) hydrogen bonds : bond 0.03492 / 2.54 ( 123) hydrogen bonds : angle 6.55398 / 4.44 ( 324) link_BETA1-4 : bond 0.00104 / 0.05 ( 1) link_BETA1-4 : angle 0.92747 / 0.52 ( 3) link_NAG-ASN : bond 0.00175 / 0.09 ( 1) link_NAG-ASN : angle 2.84322 / 1.51 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1276 Ramachandran restraints generated. 638 Oldfield, 0 Emsley, 638 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 131 time to evaluate : 0.187 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 43 LYS cc_start: 0.9276 (mmmt) cc_final: 0.8951 (mmtm) REVERT: C 72 ARG cc_start: 0.8735 (ptm160) cc_final: 0.8439 (ptm160) REVERT: C 73 ASP cc_start: 0.8569 (t70) cc_final: 0.7553 (t0) REVERT: C 83 MET cc_start: 0.7716 (mtt) cc_final: 0.7412 (mtt) REVERT: C 87 ARG cc_start: 0.7901 (mtp-110) cc_final: 0.7419 (mtp-110) REVERT: C 89 GLU cc_start: 0.7707 (mp0) cc_final: 0.7223 (mp0) REVERT: G 353 TRP cc_start: 0.8872 (p-90) cc_final: 0.8630 (p-90) REVERT: G 378 LYS cc_start: 0.8914 (mttm) cc_final: 0.8316 (mtmm) REVERT: G 462 LYS cc_start: 0.8906 (pttt) cc_final: 0.8671 (pttm) REVERT: L 2 ILE cc_start: 0.9075 (OUTLIER) cc_final: 0.8829 (mt) REVERT: L 100 LYS cc_start: 0.8872 (tmtt) cc_final: 0.8583 (tmtt) REVERT: H 73 ASP cc_start: 0.7264 (t0) cc_final: 0.6572 (t0) REVERT: H 76 MET cc_start: 0.8301 (mpp) cc_final: 0.7863 (mpp) REVERT: H 87 ARG cc_start: 0.7848 (mpp80) cc_final: 0.7592 (ptp-170) REVERT: H 106 SER cc_start: 0.9047 (t) cc_final: 0.8843 (t) outliers start: 27 outliers final: 25 residues processed: 146 average time/residue: 0.0657 time to fit residues: 12.5135 Evaluate side-chains 154 residues out of total 552 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 128 time to evaluate : 0.180 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 11 LEU Chi-restraints excluded: chain C residue 19 ARG Chi-restraints excluded: chain C residue 28 THR Chi-restraints excluded: chain C residue 35 HIS Chi-restraints excluded: chain C residue 99 HIS Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 105 LEU Chi-restraints excluded: chain E residue 11 LEU Chi-restraints excluded: chain E residue 17 ASP Chi-restraints excluded: chain E residue 72 THR Chi-restraints excluded: chain E residue 93 SER Chi-restraints excluded: chain E residue 97 THR Chi-restraints excluded: chain G residue 333 THR Chi-restraints excluded: chain G residue 335 LEU Chi-restraints excluded: chain G residue 427 ASP Chi-restraints excluded: chain G residue 468 ILE Chi-restraints excluded: chain G residue 494 SER Chi-restraints excluded: chain G residue 517 LEU Chi-restraints excluded: chain L residue 2 ILE Chi-restraints excluded: chain L residue 46 PHE Chi-restraints excluded: chain H residue 31 THR Chi-restraints excluded: chain H residue 42 GLU Chi-restraints excluded: chain H residue 69 THR Chi-restraints excluded: chain H residue 71 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 117 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 63 random chunks: chunk 23 optimal weight: 1.9990 chunk 35 optimal weight: 0.0980 chunk 11 optimal weight: 3.9990 chunk 38 optimal weight: 0.8980 chunk 12 optimal weight: 0.2980 chunk 62 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.8980 chunk 59 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 overall best weight: 0.4538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** G 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3413 r_free = 0.3413 target = 0.112650 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.095289 restraints weight = 10632.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.098402 restraints weight = 6002.099| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.100538 restraints weight = 4084.706| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.102019 restraints weight = 3102.673| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.102992 restraints weight = 2527.562| |-----------------------------------------------------------------------------| r_work (final): 0.3274 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3275 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3275 r_free = 0.3275 target_work(ls_wunit_k1) = 0.103 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (9 function evaluations) r_final: 0.3275 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.4116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5164 Z= 0.127 Angle : 0.683 8.636 7023 Z= 0.355 Chirality : 0.045 0.220 763 Planarity : 0.004 0.053 891 Dihedral : 5.778 76.462 712 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.27 % Favored : 93.73 % Rotamer: Outliers : 3.26 % Allowed : 29.71 % Favored : 67.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.00 % 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: -2.37 (0.32), residues: 638 helix: -3.28 (0.85), residues: 27 sheet: -0.93 (0.35), residues: 219 loop : -1.89 (0.30), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG E 18 TYR 0.016 0.001 TYR E 94 PHE 0.015 0.001 PHE G 347 TRP 0.012 0.001 TRP C 106 HIS 0.005 0.001 HIS C 99 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.13 ( 5154) covalent geometry : angle 0.67689 / 0.35 ( 7001) SS BOND : bond 0.00481 / 0.31 ( 8) SS BOND : angle 1.62887 / 0.78 ( 16) hydrogen bonds : bond 0.03138 / 2.28 ( 123) hydrogen bonds : angle 6.35364 / 4.29 ( 324) link_BETA1-4 : bond 0.00350 / 0.18 ( 1) link_BETA1-4 : angle 0.85817 / 0.49 ( 3) link_NAG-ASN : bond 0.00015 / 0.01 ( 1) link_NAG-ASN : angle 2.69096 / 1.44 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1220.42 seconds wall clock time: 21 minutes 47.67 seconds (1307.67 seconds total)