Starting phenix.real_space_refine on Thu Feb 13 08:51:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8txq_41703/02_2025/8txq_41703.cif Found real_map, /net/cci-nas-00/data/ceres_data/8txq_41703/02_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_41703/02_2025/8txq_41703.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8txq_41703/02_2025/8txq_41703.map" model { file = "/net/cci-nas-00/data/ceres_data/8txq_41703/02_2025/8txq_41703.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8txq_41703/02_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-5592/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: 4.35, 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: 1.85 Conformation dependent library (CDL) restraints added in 813.4 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: 0.81 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: 2.71 Time building geometry restraints manager: 2.28 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: 0.930 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: 0.150 Extract box with map and model: 0.290 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 20.700 Find NCS groups from input model: 0.060 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: 0.010 Load rotamer database and sin/cos tables:2.570 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.870 ------------------------------------------------------------------------------- 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 4667 Z= 0.308 Angle : 0.688 9.902 6371 Z= 0.389 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 *********************** 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 : 0.681 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 59 average time/residue: 0.2928 time to fit residues: 23.1787 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 : 0.691 ------------------------------------------------------------------------------- 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 4667 Z= 0.255 Angle : 0.601 5.944 6371 Z= 0.308 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 *********************** 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 : 0.596 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: 0.2603 time to fit residues: 25.5228 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 : 0.732 ------------------------------------------------------------------------------- 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 4667 Z= 0.298 Angle : 0.612 6.222 6371 Z= 0.315 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 *********************** 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 : 0.691 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: 0.2762 time to fit residues: 29.0248 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 : 0.658 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.5184 ------------------------------------------------------------------------------- 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 = 0.4106 r_free = 0.4106 target = 0.183465 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.149056 restraints weight = 15987.371| |-----------------------------------------------------------------------------| r_work (start): 0.3745 rms_B_bonded: 2.58 r_work: 0.3636 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.76 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7348 moved from start: 0.1432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4667 Z= 0.184 Angle : 0.557 6.054 6371 Z= 0.282 Chirality : 0.046 0.136 706 Planarity : 0.004 0.040 827 Dihedral : 5.170 58.686 656 Min Nonbonded Distance : 2.375 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 *********************** 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 : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8705 (OUTLIER) cc_final: 0.7410 (mp0) outliers start: 21 outliers final: 15 residues processed: 76 average time/residue: 0.2879 time to fit residues: 29.4169 Evaluate side-chains 74 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.712 ------------------------------------------------------------------------------- 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: 0.5980 chunk 32 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 42 optimal weight: 4.9990 chunk 6 optimal weight: 1.9990 chunk 7 optimal weight: 0.8980 chunk 39 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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 = 0.4081 r_free = 0.4081 target = 0.181315 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.146469 restraints weight = 16010.585| |-----------------------------------------------------------------------------| r_work (start): 0.3738 rms_B_bonded: 2.60 r_work: 0.3627 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4667 Z= 0.226 Angle : 0.570 6.015 6371 Z= 0.289 Chirality : 0.046 0.140 706 Planarity : 0.004 0.043 827 Dihedral : 5.186 58.896 656 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.67 % Favored : 88.33 % Rotamer: Outliers : 4.69 % Allowed : 18.78 % 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: -2.72 (0.33), residues: 600 helix: -0.97 (1.15), residues: 24 sheet: -0.58 (0.37), residues: 215 loop : -2.80 (0.29), residues: 361 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 0.008 0.001 PHE C 509 TYR 0.007 0.001 TYR B 37 ARG 0.001 0.000 ARG B 62 *********************** 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 82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 59 time to evaluate : 0.672 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8702 (OUTLIER) cc_final: 0.7419 (mp0) REVERT: C 637 GLU cc_start: 0.7977 (tm-30) cc_final: 0.7684 (tm-30) outliers start: 23 outliers final: 22 residues processed: 81 average time/residue: 0.2771 time to fit residues: 30.1211 Evaluate side-chains 78 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 55 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 117 THR Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 159 SER 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 44 optimal weight: 2.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 chunk 34 optimal weight: 0.0980 chunk 45 optimal weight: 0.9980 chunk 32 optimal weight: 10.0000 chunk 6 optimal weight: 0.5980 chunk 26 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4087 r_free = 0.4087 target = 0.181970 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.147237 restraints weight = 16005.665| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.59 r_work: 0.3600 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.3450 rms_B_bonded: 4.72 restraints_weight: 0.2500 r_work (final): 0.3450 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7360 moved from start: 0.1702 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4667 Z= 0.205 Angle : 0.559 5.989 6371 Z= 0.283 Chirality : 0.046 0.138 706 Planarity : 0.004 0.041 827 Dihedral : 5.145 59.244 656 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.50 % Favored : 89.50 % Rotamer: Outliers : 5.71 % Allowed : 17.96 % 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: -2.68 (0.33), residues: 600 helix: -0.89 (1.17), residues: 24 sheet: -0.53 (0.37), residues: 215 loop : -2.81 (0.29), residues: 361 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 0.008 0.001 PHE C 509 TYR 0.007 0.001 TYR C 611 ARG 0.002 0.000 ARG A 23 *********************** 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 86 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.702 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8685 (OUTLIER) cc_final: 0.7510 (mp0) REVERT: A 23 ARG cc_start: 0.7781 (OUTLIER) cc_final: 0.7530 (ttm-80) REVERT: C 637 GLU cc_start: 0.7938 (tm-30) cc_final: 0.7614 (tm-30) outliers start: 28 outliers final: 26 residues processed: 84 average time/residue: 0.2989 time to fit residues: 33.1455 Evaluate side-chains 82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 54 time to evaluate : 0.723 ------------------------------------------------------------------------------- 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 54 optimal weight: 1.9990 chunk 42 optimal weight: 0.9990 chunk 21 optimal weight: 0.9990 chunk 34 optimal weight: 3.9990 chunk 1 optimal weight: 2.9990 chunk 32 optimal weight: 9.9990 chunk 55 optimal weight: 1.9990 chunk 44 optimal weight: 0.6980 chunk 40 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 0.9980 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.4084 r_free = 0.4084 target = 0.181402 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.146639 restraints weight = 16213.302| |-----------------------------------------------------------------------------| r_work (start): 0.3706 rms_B_bonded: 2.61 r_work: 0.3596 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3449 rms_B_bonded: 4.80 restraints_weight: 0.2500 r_work (final): 0.3449 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.1869 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4667 Z= 0.263 Angle : 0.581 6.048 6371 Z= 0.296 Chirality : 0.046 0.142 706 Planarity : 0.005 0.043 827 Dihedral : 5.246 59.181 656 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 6.10 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.33 % Favored : 87.50 % Rotamer: Outliers : 5.71 % Allowed : 17.96 % 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: -2.72 (0.33), residues: 600 helix: -1.12 (1.13), residues: 24 sheet: -0.49 (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 0.008 0.001 PHE C 509 TYR 0.009 0.001 TYR B 37 ARG 0.002 0.000 ARG B 62 *********************** 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 88 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 60 time to evaluate : 0.734 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8677 (OUTLIER) cc_final: 0.7461 (mp0) REVERT: A 23 ARG cc_start: 0.7777 (OUTLIER) cc_final: 0.7566 (ttm-80) REVERT: C 555 MET cc_start: 0.6583 (tpt) cc_final: 0.6371 (tpt) REVERT: C 637 GLU cc_start: 0.7947 (tm-30) cc_final: 0.7608 (tm-30) outliers start: 28 outliers final: 26 residues processed: 86 average time/residue: 0.2908 time to fit residues: 33.1464 Evaluate side-chains 86 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 58 time to evaluate : 0.694 ------------------------------------------------------------------------------- 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 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 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: 0.9990 chunk 16 optimal weight: 1.9990 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.0270 chunk 58 optimal weight: 1.9990 chunk 45 optimal weight: 0.0020 chunk 59 optimal weight: 0.1980 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9990 chunk 17 optimal weight: 0.2980 chunk 30 optimal weight: 0.9980 overall best weight: 0.2646 ------------------------------------------------------------------------------- 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 = 0.4105 r_free = 0.4105 target = 0.183947 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.149328 restraints weight = 16239.724| |-----------------------------------------------------------------------------| r_work (start): 0.3743 rms_B_bonded: 2.61 r_work: 0.3635 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3490 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.3490 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7315 moved from start: 0.1867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 4667 Z= 0.161 Angle : 0.538 5.875 6371 Z= 0.271 Chirality : 0.045 0.132 706 Planarity : 0.004 0.036 827 Dihedral : 5.035 59.967 656 Min Nonbonded Distance : 2.326 Molprobity Statistics. All-atom Clashscore : 4.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.83 % Favored : 90.17 % Rotamer: Outliers : 3.88 % Allowed : 19.80 % 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: -2.54 (0.33), residues: 600 helix: -0.89 (1.18), residues: 24 sheet: -0.33 (0.38), residues: 205 loop : -2.72 (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 C 611 ARG 0.002 0.000 ARG B 24 *********************** 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 79 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 60 time to evaluate : 0.811 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8661 (OUTLIER) cc_final: 0.7438 (mp0) REVERT: A 39 GLN cc_start: 0.8408 (OUTLIER) cc_final: 0.7898 (tt0) outliers start: 19 outliers final: 15 residues processed: 78 average time/residue: 0.3136 time to fit residues: 32.4545 Evaluate side-chains 74 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 57 time to evaluate : 0.672 ------------------------------------------------------------------------------- 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 52 VAL 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 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 583 THR Chi-restraints excluded: chain C residue 610 ASP 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 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: 1.9990 chunk 29 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 5.9990 chunk 43 optimal weight: 0.9990 chunk 6 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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 = 0.4064 r_free = 0.4064 target = 0.179780 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3710 r_free = 0.3710 target = 0.144903 restraints weight = 16319.963| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.62 r_work: 0.3566 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3418 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7428 moved from start: 0.1996 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4667 Z= 0.293 Angle : 0.603 6.077 6371 Z= 0.309 Chirality : 0.047 0.147 706 Planarity : 0.005 0.043 827 Dihedral : 5.270 59.843 656 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 6.44 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.50 % Favored : 87.33 % Rotamer: Outliers : 4.90 % Allowed : 18.78 % 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: -2.68 (0.33), residues: 600 helix: -1.23 (1.12), residues: 24 sheet: -0.41 (0.38), 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 B 63 TYR 0.011 0.001 TYR B 37 ARG 0.002 0.000 ARG B 62 *********************** 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 85 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 61 time to evaluate : 0.687 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8660 (OUTLIER) cc_final: 0.7483 (mp0) REVERT: A 23 ARG cc_start: 0.7869 (OUTLIER) cc_final: 0.7631 (ttm-80) REVERT: C 555 MET cc_start: 0.6156 (OUTLIER) cc_final: 0.5178 (tpt) REVERT: C 637 GLU cc_start: 0.7959 (tm-30) cc_final: 0.7699 (tm-30) outliers start: 24 outliers final: 19 residues processed: 82 average time/residue: 0.2915 time to fit residues: 32.2418 Evaluate side-chains 82 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 60 time to evaluate : 1.080 ------------------------------------------------------------------------------- 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 156 VAL Chi-restraints excluded: chain A residue 157 THR Chi-restraints excluded: chain A residue 188 VAL 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 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 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: 0.9980 chunk 39 optimal weight: 0.8980 chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 0.0020 chunk 32 optimal weight: 0.8980 chunk 25 optimal weight: 0.9980 chunk 16 optimal weight: 1.9990 chunk 45 optimal weight: 0.9980 chunk 42 optimal weight: 0.4980 chunk 41 optimal weight: 1.9990 chunk 27 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 = 0.4080 r_free = 0.4080 target = 0.181570 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.146955 restraints weight = 16222.193| |-----------------------------------------------------------------------------| r_work (start): 0.3739 rms_B_bonded: 2.61 r_work: 0.3629 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3481 rms_B_bonded: 4.81 restraints_weight: 0.2500 r_work (final): 0.3481 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7358 moved from start: 0.2019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4667 Z= 0.201 Angle : 0.570 6.033 6371 Z= 0.288 Chirality : 0.046 0.138 706 Planarity : 0.004 0.038 827 Dihedral : 5.170 59.122 656 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 6.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.83 % Favored : 89.17 % Rotamer: Outliers : 3.67 % Allowed : 20.20 % 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: -2.60 (0.33), residues: 600 helix: -1.14 (1.15), residues: 24 sheet: -0.35 (0.38), 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 0.007 0.001 PHE C 509 TYR 0.006 0.001 TYR A 109 ARG 0.001 0.000 ARG B 55 ********************** 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 78 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 60 time to evaluate : 0.640 Fit side-chains revert: symmetry clash REVERT: A 10 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.7504 (mp0) REVERT: A 23 ARG cc_start: 0.7770 (OUTLIER) cc_final: 0.7526 (ttm-80) REVERT: C 555 MET cc_start: 0.6086 (OUTLIER) cc_final: 0.5169 (tpt) REVERT: C 637 GLU cc_start: 0.7931 (tm-30) cc_final: 0.7652 (tm-30) outliers start: 18 outliers final: 15 residues processed: 76 average time/residue: 0.3035 time to fit residues: 30.3465 Evaluate side-chains 76 residues out of total 515 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 58 time to evaluate : 0.675 ------------------------------------------------------------------------------- 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 157 THR 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 555 MET Chi-restraints excluded: chain C residue 583 THR Chi-restraints excluded: chain C residue 610 ASP 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 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: 2.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 1.9990 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: 0.8980 chunk 19 optimal weight: 1.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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 = 0.4075 r_free = 0.4075 target = 0.180812 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.146331 restraints weight = 16292.400| |-----------------------------------------------------------------------------| r_work (start): 0.3683 rms_B_bonded: 2.59 r_work: 0.3572 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7393 moved from start: 0.2110 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4667 Z= 0.250 Angle : 0.592 6.237 6371 Z= 0.300 Chirality : 0.046 0.144 706 Planarity : 0.005 0.041 827 Dihedral : 5.215 58.795 656 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 6.78 Ramachandran Plot: Outliers : 0.17 % Allowed : 12.00 % Favored : 87.83 % Rotamer: Outliers : 4.49 % Allowed : 19.80 % 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: -2.68 (0.33), residues: 600 helix: -1.29 (1.13), residues: 24 sheet: -0.38 (0.38), residues: 213 loop : -2.87 (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 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5382.86 seconds wall clock time: 95 minutes 12.47 seconds (5712.47 seconds total)