Starting phenix.real_space_refine on Mon May 12 08:15:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txq_41703/05_2025/8txq_41703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txq_41703/05_2025/8txq_41703.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8txq_41703/05_2025/8txq_41703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txq_41703/05_2025/8txq_41703.map" model { file = "/net/cci-nas-00/data/ceres_data/8txq_41703/05_2025/8txq_41703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txq_41703/05_2025/8txq_41703.cif" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.042 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: 5 Type Number sf(0) Gaussians S 27 5.16 5 C 2871 2.51 5 N 772 2.21 5 O 876 1.98 5 H 4305 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 8851 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3223 Number of conformers: 1 Conformer: "" Number of residues, atoms: 220, 3223 Classifications: {'peptide': 220} Link IDs: {'PTRANS': 13, 'TRANS': 206} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "B" Number of atoms: 1554 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 1554 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 7, 'TRANS': 98} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 2522 Number of conformers: 1 Conformer: "" Number of residues, atoms: 180, 2522 Classifications: {'peptide': 180} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 160} Chain breaks: 1 Unresolved non-hydrogen bonds: 85 Unresolved non-hydrogen angles: 109 Unresolved non-hydrogen dihedrals: 74 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 2, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 70 Chain: "E" Number of atoms: 1552 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 1552 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 4.33, per 1000 atoms: 0.49 Number of scatterers: 8851 At special positions: 0 Unit cell: (70.56, 100.8, 116.48, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 27 16.00 O 876 8.00 N 772 7.00 C 2871 6.00 H 4305 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=11, symmetry=0 Simple disulfide: pdb=" SG CYS A 22 " - pdb=" SG CYS A 96 " distance=2.03 Simple disulfide: pdb=" SG CYS A 146 " - pdb=" SG CYS A 202 " distance=2.03 Simple disulfide: pdb=" SG CYS B 23 " - pdb=" SG CYS B 89 " distance=2.04 Simple disulfide: pdb=" SG CYS C 452 " - pdb=" SG CYS C 620 " distance=2.03 Simple disulfide: pdb=" SG CYS C 459 " - pdb=" SG CYS C 486 " distance=2.03 Simple disulfide: pdb=" SG CYS C 494 " - pdb=" SG CYS C 564 " distance=2.03 Simple disulfide: pdb=" SG CYS C 508 " - pdb=" SG CYS C 552 " distance=2.04 Simple disulfide: pdb=" SG CYS C 569 " - pdb=" SG CYS C 597 " distance=2.03 Simple disulfide: pdb=" SG CYS C 581 " - pdb=" SG CYS C 585 " distance=2.03 Simple disulfide: pdb=" SG CYS C 607 " - pdb=" SG CYS C 644 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " 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 Time building additional restraints: 2.04 Conformation dependent library (CDL) restraints added in 709.6 milliseconds 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1104 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 12 sheets defined 8.0% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.74 Creating SS restraints... Processing helix chain 'A' and resid 62 through 65 removed outlier: 3.967A pdb=" N GLN A 65 " --> pdb=" O GLN A 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 62 through 65' Processing helix chain 'A' and resid 87 through 91 removed outlier: 3.878A pdb=" N THR A 91 " --> pdb=" O PHE A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 207 through 210 Processing helix chain 'B' and resid 80 through 84 removed outlier: 3.902A pdb=" N PHE B 84 " --> pdb=" O PRO B 81 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 547 Processing helix chain 'C' and resid 593 through 598 Processing helix chain 'C' and resid 613 through 618 Processing helix chain 'E' and resid 121 through 128 removed outlier: 3.893A pdb=" N LYS E 126 " --> pdb=" O ASP E 122 " (cutoff:3.500A) Processing helix chain 'E' and resid 182 through 187 Processing sheet with id=AA1, first strand: chain 'A' and resid 2 through 3 removed outlier: 3.753A pdb=" N ILE A 2 " --> pdb=" O SER A 25 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 11 through 12 removed outlier: 3.530A pdb=" N TYR A 94 " --> pdb=" O THR A 117 " (cutoff:3.500A) removed outlier: 3.752A pdb=" N VAL A 37 " --> pdb=" O TYR A 95 " (cutoff:3.500A) removed outlier: 6.768A pdb=" N ILE A 34 " --> pdb=" O GLY A 50 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N GLY A 50 " --> pdb=" O ILE A 34 " (cutoff:3.500A) removed outlier: 6.676A pdb=" N TRP A 36 " --> pdb=" O VAL A 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 103 through 104 Processing sheet with id=AA4, first strand: chain 'A' and resid 128 through 130 removed outlier: 3.804A pdb=" N GLY A 145 " --> pdb=" O LEU A 130 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N SER A 186 " --> pdb=" O CYS A 146 " (cutoff:3.500A) removed outlier: 6.583A pdb=" N TYR A 182 " --> pdb=" O ASP A 150 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 157 through 158 removed outlier: 3.621A pdb=" N LYS A 215 " --> pdb=" O CYS A 202 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N THR A 211 " --> pdb=" O HIS A 206 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 4 through 5 removed outlier: 3.746A pdb=" N THR B 5 " --> pdb=" O ARG B 24 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 10 through 11 removed outlier: 3.762A pdb=" N LEU B 11 " --> pdb=" O LYS B 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'B' and resid 54 through 55 removed outlier: 3.526A pdb=" N ILE B 54 " --> pdb=" O TYR B 50 " (cutoff:3.500A) removed outlier: 5.845A pdb=" N LEU B 47 " --> pdb=" O GLN B 38 " (cutoff:3.500A) removed outlier: 6.861A pdb=" N GLN B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 3.512A pdb=" N ILE B 49 " --> pdb=" O TRP B 36 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'C' and resid 473 through 474 removed outlier: 3.669A pdb=" N THR C 473 " --> pdb=" O ASN C 570 " (cutoff:3.500A) removed outlier: 3.893A pdb=" N ASN C 570 " --> pdb=" O THR C 473 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'C' and resid 513 through 515 removed outlier: 4.978A pdb=" N TYR C 507 " --> pdb=" O THR C 553 " (cutoff:3.500A) removed outlier: 4.275A pdb=" N THR C 553 " --> pdb=" O TYR C 507 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N GLY C 551 " --> pdb=" O PHE C 509 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.780A pdb=" N ASN E 138 " --> pdb=" O TYR E 173 " (cutoff:3.500A) removed outlier: 7.041A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 153 through 154 122 hydrogen bonds defined for protein. 300 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: 2.63 Time building geometry restraints manager: 2.50 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 4304 1.02 - 1.23: 21 1.23 - 1.43: 2035 1.43 - 1.64: 2581 1.64 - 1.84: 31 Bond restraints: 8972 Sorted by residual: bond pdb=" C ALA E 193 " pdb=" O ALA E 193 " ideal model delta sigma weight residual 1.234 1.130 0.104 1.19e-02 7.06e+03 7.68e+01 bond pdb=" CA VAL E 191 " pdb=" CB VAL E 191 " ideal model delta sigma weight residual 1.550 1.470 0.080 1.03e-02 9.43e+03 6.06e+01 bond pdb=" CA VAL E 191 " pdb=" C VAL E 191 " ideal model delta sigma weight residual 1.520 1.464 0.056 1.17e-02 7.31e+03 2.29e+01 bond pdb=" C VAL E 191 " pdb=" O VAL E 191 " ideal model delta sigma weight residual 1.234 1.179 0.055 1.21e-02 6.83e+03 2.08e+01 bond pdb=" CA TYR E 192 " pdb=" CB TYR E 192 " ideal model delta sigma weight residual 1.534 1.472 0.062 1.77e-02 3.19e+03 1.22e+01 ... (remaining 8967 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 15991 1.98 - 3.96: 125 3.96 - 5.94: 26 5.94 - 7.92: 5 7.92 - 9.90: 4 Bond angle restraints: 16151 Sorted by residual: angle pdb=" N LYS E 190 " pdb=" CA LYS E 190 " pdb=" C LYS E 190 " ideal model delta sigma weight residual 110.61 120.09 -9.48 1.25e+00 6.40e-01 5.76e+01 angle pdb=" N TYR E 192 " pdb=" CA TYR E 192 " pdb=" C TYR E 192 " ideal model delta sigma weight residual 109.14 99.24 9.90 1.49e+00 4.50e-01 4.42e+01 angle pdb=" N VAL E 191 " pdb=" CA VAL E 191 " pdb=" C VAL E 191 " ideal model delta sigma weight residual 107.88 99.28 8.60 1.38e+00 5.25e-01 3.89e+01 angle pdb=" N ALA E 193 " pdb=" CA ALA E 193 " pdb=" C ALA E 193 " ideal model delta sigma weight residual 108.42 117.40 -8.98 1.54e+00 4.22e-01 3.40e+01 angle pdb=" CA ALA E 193 " pdb=" C ALA E 193 " pdb=" N CYS E 194 " ideal model delta sigma weight residual 115.38 121.07 -5.69 1.40e+00 5.10e-01 1.65e+01 ... (remaining 16146 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.20: 3817 17.20 - 34.39: 388 34.39 - 51.59: 135 51.59 - 68.79: 32 68.79 - 85.98: 5 Dihedral angle restraints: 4377 sinusoidal: 2318 harmonic: 2059 Sorted by residual: dihedral pdb=" CB CYS C 508 " pdb=" SG CYS C 508 " pdb=" SG CYS C 552 " pdb=" CB CYS C 552 " ideal model delta sinusoidal sigma weight residual 93.00 12.06 80.94 1 1.00e+01 1.00e-02 8.09e+01 dihedral pdb=" CB CYS C 452 " pdb=" SG CYS C 452 " pdb=" SG CYS C 620 " pdb=" CB CYS C 620 " ideal model delta sinusoidal sigma weight residual -86.00 -163.38 77.38 1 1.00e+01 1.00e-02 7.50e+01 dihedral pdb=" CB CYS C 494 " pdb=" SG CYS C 494 " pdb=" SG CYS C 564 " pdb=" CB CYS C 564 " ideal model delta sinusoidal sigma weight residual 93.00 160.42 -67.42 1 1.00e+01 1.00e-02 5.91e+01 ... (remaining 4374 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 462 0.037 - 0.074: 158 0.074 - 0.111: 59 0.111 - 0.148: 24 0.148 - 0.185: 3 Chirality restraints: 706 Sorted by residual: chirality pdb=" CA LYS E 190 " pdb=" N LYS E 190 " pdb=" C LYS E 190 " pdb=" CB LYS E 190 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.58e-01 chirality pdb=" CA HIS E 189 " pdb=" N HIS E 189 " pdb=" C HIS E 189 " pdb=" CB HIS E 189 " both_signs ideal model delta sigma weight residual False 2.51 2.67 -0.16 2.00e-01 2.50e+01 6.44e-01 chirality pdb=" CA ALA E 193 " pdb=" N ALA E 193 " pdb=" C ALA E 193 " pdb=" CB ALA E 193 " both_signs ideal model delta sigma weight residual False 2.48 2.33 0.15 2.00e-01 2.50e+01 5.71e-01 ... (remaining 703 not shown) Planarity restraints: 1388 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA E 193 " -0.031 2.00e-02 2.50e+03 5.87e-02 3.45e+01 pdb=" N CYS E 194 " 0.101 2.00e-02 2.50e+03 pdb=" CA CYS E 194 " -0.025 2.00e-02 2.50e+03 pdb=" H CYS E 194 " -0.046 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL E 191 " -0.016 2.00e-02 2.50e+03 3.10e-02 9.62e+00 pdb=" C VAL E 191 " 0.054 2.00e-02 2.50e+03 pdb=" O VAL E 191 " -0.020 2.00e-02 2.50e+03 pdb=" N TYR E 192 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS E 188 " 0.014 2.00e-02 2.50e+03 2.82e-02 7.95e+00 pdb=" C LYS E 188 " -0.049 2.00e-02 2.50e+03 pdb=" O LYS E 188 " 0.019 2.00e-02 2.50e+03 pdb=" N HIS E 189 " 0.016 2.00e-02 2.50e+03 ... (remaining 1385 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.22: 902 2.22 - 2.82: 17784 2.82 - 3.41: 20794 3.41 - 4.01: 28822 4.01 - 4.60: 43556 Nonbonded interactions: 111858 Sorted by model distance: nonbonded pdb=" OD1 ASP A 101 " pdb=" HG SER A 108 " model vdw 1.627 2.450 nonbonded pdb=" HG1 THR C 583 " pdb=" O TRP C 602 " model vdw 1.663 2.450 nonbonded pdb=" HG SER A 134 " pdb=" OG1 THR A 137 " model vdw 1.668 2.450 nonbonded pdb=" H TRP C 469 " pdb=" O GLY C 572 " model vdw 1.672 2.450 nonbonded pdb=" OE1 GLN B 38 " pdb="HH21 ARG B 46 " model vdw 1.707 2.450 ... (remaining 111853 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.830 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.140 Extract box with map and model: 0.280 Check model and map are aligned: 0.050 Set scattering table: 0.080 Process input model: 20.440 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.550 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7054 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 : 0.004 0.104 4678 Z= 0.270 Angle : 0.691 9.902 6393 Z= 0.390 Chirality : 0.047 0.185 706 Planarity : 0.004 0.044 827 Dihedral : 15.338 85.985 1634 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 0.41 % Allowed : 22.24 % Favored : 77.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.34), residues: 600 helix: -1.94 (0.95), residues: 24 sheet: -0.82 (0.36), residues: 212 loop : -2.51 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS E 198 PHE 0.006 0.001 PHE E 209 TYR 0.010 0.001 TYR E 192 ARG 0.001 0.000 ARG C 639 Details of bonding type rmsd hydrogen bonds : bond 0.19424 ( 122) hydrogen bonds : angle 7.83957 ( 300) SS BOND : bond 0.00465 ( 11) SS BOND : angle 1.22326 ( 22) covalent geometry : bond 0.00431 ( 4667) covalent geometry : angle 0.68815 ( 6371) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 59 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 57 time to evaluate : 0.761 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.2848 time to fit residues: 22.7368 Evaluate side-chains 56 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 55 time to evaluate : 0.771 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 191 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 15 optimal weight: 0.9990 chunk 30 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 47 optimal weight: 4.9990 chunk 18 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4100 r_free = 0.4100 target = 0.182640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3747 r_free = 0.3747 target = 0.147990 restraints weight = 15943.857| |-----------------------------------------------------------------------------| r_work (start): 0.3734 rms_B_bonded: 2.57 r_work: 0.3623 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3476 rms_B_bonded: 4.85 restraints_weight: 0.2500 r_work (final): 0.3476 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7388 moved from start: 0.0814 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4678 Z= 0.154 Angle : 0.604 5.944 6393 Z= 0.309 Chirality : 0.046 0.140 706 Planarity : 0.004 0.042 827 Dihedral : 5.177 58.059 656 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 5.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 2.86 % Allowed : 20.41 % Favored : 76.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.76 (0.33), residues: 600 helix: -1.34 (1.12), residues: 24 sheet: -0.55 (0.38), residues: 200 loop : -2.77 (0.29), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 148 HIS 0.005 0.001 HIS E 189 PHE 0.009 0.001 PHE C 509 TYR 0.009 0.001 TYR B 37 ARG 0.001 0.000 ARG B 46 Details of bonding type rmsd hydrogen bonds : bond 0.03793 ( 122) hydrogen bonds : angle 6.52762 ( 300) SS BOND : bond 0.00435 ( 11) SS BOND : angle 1.14418 ( 22) covalent geometry : bond 0.00373 ( 4667) covalent geometry : angle 0.60087 ( 6371) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 75 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 61 time to evaluate : 0.687 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8723 (OUTLIER) cc_final: 0.7362 (mp0) REVERT: C 591 GLU cc_start: 0.7707 (tm-30) cc_final: 0.7265 (tm-30) outliers start: 14 outliers final: 8 residues processed: 72 average time/residue: 0.2545 time to fit residues: 25.2478 Evaluate side-chains 69 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 191 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 47 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 chunk 43 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 38 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 39 optimal weight: 0.9980 chunk 56 optimal weight: 3.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.179498 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.144531 restraints weight = 16291.451| |-----------------------------------------------------------------------------| r_work (start): 0.3671 rms_B_bonded: 2.63 r_work: 0.3560 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3410 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3410 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.1313 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 4678 Z= 0.181 Angle : 0.615 6.222 6393 Z= 0.316 Chirality : 0.047 0.145 706 Planarity : 0.005 0.045 827 Dihedral : 5.357 58.183 656 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 3.88 % Allowed : 20.00 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.79 (0.33), residues: 600 helix: -1.41 (1.06), residues: 24 sheet: -0.64 (0.37), residues: 213 loop : -2.81 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.004 0.001 HIS E 189 PHE 0.009 0.001 PHE E 209 TYR 0.011 0.001 TYR B 37 ARG 0.002 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.03613 ( 122) hydrogen bonds : angle 6.29390 ( 300) SS BOND : bond 0.00446 ( 11) SS BOND : angle 1.17503 ( 22) covalent geometry : bond 0.00439 ( 4667) covalent geometry : angle 0.61225 ( 6371) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 80 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 61 time to evaluate : 0.794 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 591 GLU cc_start: 0.7763 (tm-30) cc_final: 0.7404 (tm-30) outliers start: 19 outliers final: 18 residues processed: 78 average time/residue: 0.2718 time to fit residues: 29.0262 Evaluate side-chains 75 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 57 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 57 optimal weight: 1.9990 chunk 36 optimal weight: 0.6980 chunk 47 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 0.0000 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 39 optimal weight: 0.6980 overall best weight: 0.5384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4105 r_free = 0.4105 target = 0.183387 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.148905 restraints weight = 15990.023| |-----------------------------------------------------------------------------| r_work (start): 0.3726 rms_B_bonded: 2.59 r_work: 0.3617 rms_B_bonded: 2.83 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7353 moved from start: 0.1441 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4678 Z= 0.112 Angle : 0.559 6.082 6393 Z= 0.283 Chirality : 0.046 0.136 706 Planarity : 0.004 0.041 827 Dihedral : 5.168 58.666 656 Min Nonbonded Distance : 2.373 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 4.29 % Allowed : 19.59 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.75 (0.33), residues: 600 helix: -1.10 (1.12), residues: 24 sheet: -0.55 (0.37), residues: 210 loop : -2.83 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS E 189 PHE 0.007 0.001 PHE C 509 TYR 0.006 0.001 TYR A 109 ARG 0.001 0.000 ARG C 639 Details of bonding type rmsd hydrogen bonds : bond 0.02778 ( 122) hydrogen bonds : angle 5.94080 ( 300) SS BOND : bond 0.00342 ( 11) SS BOND : angle 0.92648 ( 22) covalent geometry : bond 0.00276 ( 4667) covalent geometry : angle 0.55738 ( 6371) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 78 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 57 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8691 (OUTLIER) cc_final: 0.7449 (mp0) outliers start: 21 outliers final: 15 residues processed: 76 average time/residue: 0.2951 time to fit residues: 30.2502 Evaluate side-chains 73 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 57 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 16 optimal weight: 2.9990 chunk 40 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 chunk 49 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4091 r_free = 0.4091 target = 0.182068 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3740 r_free = 0.3740 target = 0.147459 restraints weight = 16069.061| |-----------------------------------------------------------------------------| r_work (start): 0.3688 rms_B_bonded: 2.61 r_work: 0.3577 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3428 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.1640 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4678 Z= 0.150 Angle : 0.585 6.069 6393 Z= 0.298 Chirality : 0.046 0.142 706 Planarity : 0.005 0.044 827 Dihedral : 5.252 58.823 656 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.00 % Favored : 88.00 % Rotamer: Outliers : 4.90 % Allowed : 18.57 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.74 (0.33), residues: 600 helix: -0.98 (1.14), residues: 24 sheet: -0.57 (0.37), residues: 213 loop : -2.83 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 47 HIS 0.003 0.001 HIS E 189 PHE 0.007 0.001 PHE C 509 TYR 0.008 0.001 TYR B 37 ARG 0.002 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.02952 ( 122) hydrogen bonds : angle 5.87254 ( 300) SS BOND : bond 0.00423 ( 11) SS BOND : angle 1.10818 ( 22) covalent geometry : bond 0.00368 ( 4667) covalent geometry : angle 0.58278 ( 6371) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 83 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 59 time to evaluate : 0.682 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 637 GLU cc_start: 0.7980 (tm-30) cc_final: 0.7687 (tm-30) outliers start: 24 outliers final: 24 residues processed: 81 average time/residue: 0.2738 time to fit residues: 29.8649 Evaluate side-chains 80 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 56 time to evaluate : 0.652 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.4980 chunk 34 optimal weight: 0.3980 chunk 45 optimal weight: 0.2980 chunk 32 optimal weight: 9.9990 chunk 6 optimal weight: 0.9990 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4088 r_free = 0.4088 target = 0.182053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147491 restraints weight = 15997.971| |-----------------------------------------------------------------------------| r_work (start): 0.3724 rms_B_bonded: 2.57 r_work: 0.3615 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3471 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3471 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4678 Z= 0.118 Angle : 0.559 5.990 6393 Z= 0.283 Chirality : 0.046 0.137 706 Planarity : 0.004 0.040 827 Dihedral : 5.164 59.311 656 Min Nonbonded Distance : 2.325 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.67 % Favored : 89.33 % Rotamer: Outliers : 5.51 % Allowed : 17.96 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.33), residues: 600 helix: -0.94 (1.17), residues: 24 sheet: -0.52 (0.38), residues: 205 loop : -2.78 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS E 189 PHE 0.007 0.001 PHE C 509 TYR 0.007 0.001 TYR C 611 ARG 0.001 0.000 ARG A 23 Details of bonding type rmsd hydrogen bonds : bond 0.02648 ( 122) hydrogen bonds : angle 5.66067 ( 300) SS BOND : bond 0.00312 ( 11) SS BOND : angle 0.98842 ( 22) covalent geometry : bond 0.00289 ( 4667) covalent geometry : angle 0.55729 ( 6371) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 84 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 57 time to evaluate : 0.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8650 (OUTLIER) cc_final: 0.7481 (mp0) REVERT: A 23 ARG cc_start: 0.7799 (OUTLIER) cc_final: 0.7535 (ttm-80) REVERT: C 637 GLU cc_start: 0.7930 (tm-30) cc_final: 0.7607 (tm-30) outliers start: 27 outliers final: 25 residues processed: 83 average time/residue: 0.2932 time to fit residues: 32.4780 Evaluate side-chains 79 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 52 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 0.0270 chunk 42 optimal weight: 0.6980 chunk 21 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 53 optimal weight: 0.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4087 r_free = 0.4087 target = 0.181812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147168 restraints weight = 16140.073| |-----------------------------------------------------------------------------| r_work (start): 0.3710 rms_B_bonded: 2.59 r_work: 0.3597 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7371 moved from start: 0.1821 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4678 Z= 0.128 Angle : 0.565 5.989 6393 Z= 0.286 Chirality : 0.046 0.139 706 Planarity : 0.004 0.041 827 Dihedral : 5.156 59.570 656 Min Nonbonded Distance : 2.364 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.83 % Favored : 88.17 % Rotamer: Outliers : 5.71 % Allowed : 17.76 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.70 (0.33), residues: 600 helix: -1.12 (1.13), residues: 24 sheet: -0.49 (0.38), residues: 205 loop : -2.78 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS C 638 PHE 0.008 0.001 PHE C 509 TYR 0.007 0.001 TYR B 37 ARG 0.001 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.02679 ( 122) hydrogen bonds : angle 5.59310 ( 300) SS BOND : bond 0.00395 ( 11) SS BOND : angle 1.03803 ( 22) covalent geometry : bond 0.00317 ( 4667) covalent geometry : angle 0.56286 ( 6371) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 59 time to evaluate : 0.644 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7439 (mp0) REVERT: A 23 ARG cc_start: 0.7786 (OUTLIER) cc_final: 0.7535 (ttm-80) REVERT: C 637 GLU cc_start: 0.7951 (tm-30) cc_final: 0.7612 (tm-30) outliers start: 28 outliers final: 26 residues processed: 85 average time/residue: 0.2786 time to fit residues: 31.2918 Evaluate side-chains 85 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.640 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 564 CYS Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.4980 chunk 42 optimal weight: 0.2980 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 0.7980 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4083 r_free = 0.4083 target = 0.181696 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146824 restraints weight = 16302.876| |-----------------------------------------------------------------------------| r_work (start): 0.3727 rms_B_bonded: 2.63 r_work: 0.3619 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3472 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3472 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4678 Z= 0.113 Angle : 0.555 5.935 6393 Z= 0.281 Chirality : 0.045 0.138 706 Planarity : 0.004 0.039 827 Dihedral : 5.120 59.944 656 Min Nonbonded Distance : 2.342 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.17 % Favored : 89.83 % Rotamer: Outliers : 6.12 % Allowed : 17.76 % Favored : 76.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.33), residues: 600 helix: -1.02 (1.15), residues: 24 sheet: -0.41 (0.38), residues: 205 loop : -2.76 (0.29), residues: 371 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.003 0.001 HIS C 638 PHE 0.008 0.001 PHE C 509 TYR 0.006 0.001 TYR A 109 ARG 0.001 0.000 ARG B 55 Details of bonding type rmsd hydrogen bonds : bond 0.02538 ( 122) hydrogen bonds : angle 5.50461 ( 300) SS BOND : bond 0.00392 ( 11) SS BOND : angle 1.00381 ( 22) covalent geometry : bond 0.00280 ( 4667) covalent geometry : angle 0.55329 ( 6371) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 89 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 59 time to evaluate : 0.662 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8657 (OUTLIER) cc_final: 0.7425 (mp0) REVERT: A 23 ARG cc_start: 0.7801 (OUTLIER) cc_final: 0.7528 (ttm-80) REVERT: C 637 GLU cc_start: 0.7934 (tm-30) cc_final: 0.7578 (tm-30) outliers start: 30 outliers final: 26 residues processed: 87 average time/residue: 0.2997 time to fit residues: 33.9283 Evaluate side-chains 85 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 57 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 11 optimal weight: 1.9990 chunk 56 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 0.8980 chunk 29 optimal weight: 0.9980 chunk 55 optimal weight: 0.6980 chunk 25 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 0.2980 chunk 6 optimal weight: 0.9990 chunk 46 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4086 r_free = 0.4086 target = 0.182044 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.147384 restraints weight = 16214.060| |-----------------------------------------------------------------------------| r_work (start): 0.3733 rms_B_bonded: 2.60 r_work: 0.3621 rms_B_bonded: 2.86 restraints_weight: 0.5000 r_work: 0.3477 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3477 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4678 Z= 0.126 Angle : 0.569 5.985 6393 Z= 0.288 Chirality : 0.045 0.140 706 Planarity : 0.004 0.040 827 Dihedral : 5.122 59.422 656 Min Nonbonded Distance : 2.319 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.50 % Favored : 88.50 % Rotamer: Outliers : 6.12 % Allowed : 17.35 % Favored : 76.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.33), residues: 600 helix: -1.10 (1.14), residues: 24 sheet: -0.39 (0.37), residues: 213 loop : -2.81 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS C 638 PHE 0.008 0.001 PHE C 509 TYR 0.007 0.001 TYR B 37 ARG 0.001 0.000 ARG A 216 Details of bonding type rmsd hydrogen bonds : bond 0.02622 ( 122) hydrogen bonds : angle 5.50353 ( 300) SS BOND : bond 0.00405 ( 11) SS BOND : angle 1.05982 ( 22) covalent geometry : bond 0.00311 ( 4667) covalent geometry : angle 0.56637 ( 6371) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 87 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.741 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8656 (OUTLIER) cc_final: 0.7444 (mp0) REVERT: A 23 ARG cc_start: 0.7794 (OUTLIER) cc_final: 0.7534 (ttm-80) REVERT: C 555 MET cc_start: 0.6080 (OUTLIER) cc_final: 0.5147 (tpt) REVERT: C 637 GLU cc_start: 0.7954 (tm-30) cc_final: 0.7594 (tm-30) outliers start: 30 outliers final: 27 residues processed: 84 average time/residue: 0.2706 time to fit residues: 30.5957 Evaluate side-chains 87 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 57 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 2.9990 chunk 39 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 35 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 chunk 27 optimal weight: 0.4980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN C 548 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4065 r_free = 0.4065 target = 0.179915 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.145194 restraints weight = 16269.080| |-----------------------------------------------------------------------------| r_work (start): 0.3711 rms_B_bonded: 2.60 r_work: 0.3600 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3452 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.3452 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4678 Z= 0.149 Angle : 0.592 6.022 6393 Z= 0.301 Chirality : 0.046 0.145 706 Planarity : 0.005 0.041 827 Dihedral : 5.254 58.648 656 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.67 % Favored : 88.17 % Rotamer: Outliers : 6.12 % Allowed : 17.55 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.67 (0.33), residues: 600 helix: -1.21 (1.13), residues: 24 sheet: -0.40 (0.37), residues: 213 loop : -2.85 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS C 638 PHE 0.007 0.001 PHE C 509 TYR 0.009 0.001 TYR B 37 ARG 0.002 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.02803 ( 122) hydrogen bonds : angle 5.64419 ( 300) SS BOND : bond 0.00434 ( 11) SS BOND : angle 1.18476 ( 22) covalent geometry : bond 0.00366 ( 4667) covalent geometry : angle 0.58895 ( 6371) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1200 Ramachandran restraints generated. 600 Oldfield, 0 Emsley, 600 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue SER 138 is missing expected H atoms. Skipping. Residue THR 197 is missing expected H atoms. Skipping. TARDY: cannot create tardy model for: "LYS B 107 " (corrupted residue). Skipping it. Residue SER 480 is missing expected H atoms. Skipping. Residue VAL 502 is missing expected H atoms. Skipping. Residue VAL 110 is missing expected H atoms. Skipping. Residue LYS 188 is missing expected H atoms. Skipping. Evaluate side-chains 92 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 62 time to evaluate : 0.743 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8671 (OUTLIER) cc_final: 0.7459 (mp0) REVERT: A 23 ARG cc_start: 0.7797 (OUTLIER) cc_final: 0.7583 (ttm-80) REVERT: A 101 ASP cc_start: 0.8155 (t0) cc_final: 0.7658 (p0) REVERT: C 555 MET cc_start: 0.5929 (OUTLIER) cc_final: 0.5018 (tpt) REVERT: C 637 GLU cc_start: 0.7965 (tm-30) cc_final: 0.7593 (tm-30) outliers start: 30 outliers final: 27 residues processed: 89 average time/residue: 0.2789 time to fit residues: 32.9106 Evaluate side-chains 90 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 60 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 10 GLU Chi-restraints excluded: chain A residue 23 ARG Chi-restraints excluded: chain A residue 39 GLN Chi-restraints excluded: chain A residue 52 VAL Chi-restraints excluded: chain A residue 98 ARG Chi-restraints excluded: chain A residue 103 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 117 THR Chi-restraints excluded: chain A residue 156 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 SER Chi-restraints excluded: chain A residue 188 VAL Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain B residue 90 GLN Chi-restraints excluded: chain C residue 459 CYS Chi-restraints excluded: chain C residue 472 ILE Chi-restraints excluded: chain C residue 473 THR Chi-restraints excluded: chain C residue 503 CYS Chi-restraints excluded: chain C residue 539 LEU Chi-restraints excluded: chain C residue 555 MET Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP Chi-restraints excluded: chain E residue 121 SER Chi-restraints excluded: chain E residue 168 SER Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 179 LEU Chi-restraints excluded: chain E residue 191 VAL Chi-restraints excluded: chain E residue 196 VAL Chi-restraints excluded: chain E residue 201 LEU Chi-restraints excluded: chain E residue 202 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 27 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 37 optimal weight: 0.3980 chunk 11 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 5.9990 chunk 3 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 43 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4067 r_free = 0.4067 target = 0.180191 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3713 r_free = 0.3713 target = 0.145420 restraints weight = 16237.593| |-----------------------------------------------------------------------------| r_work (start): 0.3703 rms_B_bonded: 2.62 r_work: 0.3593 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3448 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3448 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 moved from start: 0.2093 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4678 Z= 0.129 Angle : 0.581 6.038 6393 Z= 0.293 Chirality : 0.045 0.140 706 Planarity : 0.004 0.039 827 Dihedral : 5.159 57.755 656 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 11.17 % Favored : 88.67 % Rotamer: Outliers : 6.12 % Allowed : 18.16 % Favored : 75.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.27 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.63 (0.33), residues: 600 helix: -1.25 (1.12), residues: 24 sheet: -0.34 (0.38), residues: 213 loop : -2.84 (0.29), residues: 363 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.002 0.001 HIS C 638 PHE 0.008 0.001 PHE C 509 TYR 0.007 0.001 TYR A 109 ARG 0.001 0.000 ARG B 62 Details of bonding type rmsd hydrogen bonds : bond 0.02620 ( 122) hydrogen bonds : angle 5.56969 ( 300) SS BOND : bond 0.00419 ( 11) SS BOND : angle 1.10522 ( 22) covalent geometry : bond 0.00317 ( 4667) covalent geometry : angle 0.57850 ( 6371) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5409.66 seconds wall clock time: 93 minutes 16.59 seconds (5596.59 seconds total)