Starting phenix.real_space_refine on Tue Feb 11 15:32:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dl8_27499/02_2025/8dl8_27499.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dl8_27499/02_2025/8dl8_27499.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8dl8_27499/02_2025/8dl8_27499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dl8_27499/02_2025/8dl8_27499.map" model { file = "/net/cci-nas-00/data/ceres_data/8dl8_27499/02_2025/8dl8_27499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dl8_27499/02_2025/8dl8_27499.cif" } resolution = 3.0 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= 0.002 sd= 0.062 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 Co 2 6.85 5 S 34 5.16 5 C 3969 2.51 5 N 1049 2.21 5 O 1154 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6208 Number of models: 1 Model: "" Number of chains: 5 Chain: "A" Number of atoms: 3387 Number of conformers: 1 Conformer: "" Number of residues, atoms: 445, 3387 Classifications: {'peptide': 445} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 433} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "C" Number of atoms: 1373 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1373 Classifications: {'peptide': 213} Incomplete info: {'truncation_to_alanine': 91} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 203} Unresolved chain link angles: 4 Unresolved non-hydrogen bonds: 290 Unresolved non-hydrogen angles: 372 Unresolved non-hydrogen dihedrals: 242 Unresolved non-hydrogen chiralities: 26 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 2, 'TYR:plan': 2, 'ASN:plan1': 7, 'TRP:plan': 2, 'ASP:plan': 6, 'PHE:plan': 3, 'GLU:plan': 7, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 154 Chain: "D" Number of atoms: 1445 Number of conformers: 1 Conformer: "" Number of residues, atoms: 219, 1445 Classifications: {'peptide': 219} Incomplete info: {'backbone_only': 4, 'truncation_to_alanine': 79} Link IDs: {'PTRANS': 14, 'TRANS': 204} Unresolved chain link angles: 9 Unresolved non-hydrogen bonds: 244 Unresolved non-hydrogen angles: 326 Unresolved non-hydrogen dihedrals: 202 Unresolved non-hydrogen chiralities: 38 Planarities with less than four sites: {'GLN:plan1': 2, 'TYR:plan': 3, 'ASN:plan1': 2, 'TRP:plan': 2, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'HIS:plan': 2} Unresolved non-hydrogen planarities: 91 Chain: "A" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' CO': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "D" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 2052 SG CYS A 326 23.364 42.046 35.119 1.00104.32 S Time building chain proxies: 4.09, per 1000 atoms: 0.66 Number of scatterers: 6208 At special positions: 0 Unit cell: (73.44, 74.52, 145.8, 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) Co 2 26.99 S 34 16.00 O 1154 8.00 N 1049 7.00 C 3969 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 367 " - pdb=" SG CYS A 553 " distance=2.03 Simple disulfide: pdb=" SG CYS C 43 " - pdb=" SG CYS C 108 " distance=2.03 Simple disulfide: pdb=" SG CYS D 41 " - pdb=" SG CYS D 115 " 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: 1.52 Conformation dependent library (CDL) restraints added in 1.0 seconds 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1604 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 8 sheets defined 49.0% alpha, 18.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.68 Creating SS restraints... Processing helix chain 'A' and resid 15 through 23 Processing helix chain 'A' and resid 23 through 54 Processing helix chain 'A' and resid 57 through 85 removed outlier: 3.745A pdb=" N THR A 61 " --> pdb=" O SER A 57 " (cutoff:3.500A) removed outlier: 5.338A pdb=" N ALA A 77 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 5.100A pdb=" N ILE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 116 removed outlier: 3.563A pdb=" N HIS A 116 " --> pdb=" O MET A 112 " (cutoff:3.500A) Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 126 through 156 removed outlier: 3.597A pdb=" N ARG A 156 " --> pdb=" O ILE A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 157 through 164 Processing helix chain 'A' and resid 166 through 199 Proline residue: A 189 - end of helix Processing helix chain 'A' and resid 200 through 230 Processing helix chain 'A' and resid 231 through 234 removed outlier: 3.740A pdb=" N ALA A 234 " --> pdb=" O PRO A 231 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 231 through 234' Processing helix chain 'A' and resid 285 through 305 removed outlier: 4.667A pdb=" N GLU A 290 " --> pdb=" O SER A 286 " (cutoff:3.500A) Proline residue: A 291 - end of helix Processing helix chain 'A' and resid 307 through 317 Processing helix chain 'A' and resid 326 through 335 removed outlier: 4.262A pdb=" N GLY A 330 " --> pdb=" O CYS A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 367 Processing helix chain 'A' and resid 368 through 392 removed outlier: 3.748A pdb=" N PHE A 392 " --> pdb=" O VAL A 388 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 483 Processing helix chain 'A' and resid 488 through 514 Processing helix chain 'A' and resid 519 through 547 Processing helix chain 'C' and resid 99 through 103 removed outlier: 4.052A pdb=" N LEU C 103 " --> pdb=" O SER C 100 " (cutoff:3.500A) Processing helix chain 'C' and resid 141 through 147 Processing helix chain 'C' and resid 202 through 208 Processing helix chain 'D' and resid 47 through 51 Processing helix chain 'D' and resid 106 through 110 removed outlier: 3.931A pdb=" N THR D 110 " --> pdb=" O SER D 107 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 24 through 25 removed outlier: 3.652A pdb=" N ASP C 90 " --> pdb=" O SER C 87 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 30 through 33 removed outlier: 6.730A pdb=" N VAL C 53 " --> pdb=" O TYR C 69 " (cutoff:3.500A) removed outlier: 4.783A pdb=" N TYR C 69 " --> pdb=" O VAL C 53 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N TRP C 55 " --> pdb=" O LEU C 67 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 135 through 138 removed outlier: 3.908A pdb=" N VAL C 153 " --> pdb=" O PHE C 138 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N ASN C 158 " --> pdb=" O TYR C 193 " (cutoff:3.500A) removed outlier: 6.199A pdb=" N TYR C 193 " --> pdb=" O ASN C 158 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 165 through 170 Processing sheet with id=AA5, first strand: chain 'D' and resid 22 through 25 Processing sheet with id=AA6, first strand: chain 'D' and resid 29 through 31 removed outlier: 6.537A pdb=" N MET D 53 " --> pdb=" O TRP D 69 " (cutoff:3.500A) removed outlier: 4.466A pdb=" N TRP D 69 " --> pdb=" O MET D 53 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N TRP D 55 " --> pdb=" O ILE D 67 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'D' and resid 145 through 149 removed outlier: 4.103A pdb=" N LEU D 166 " --> pdb=" O TYR D 147 " (cutoff:3.500A) removed outlier: 4.084A pdb=" N GLY D 164 " --> pdb=" O LEU D 149 " (cutoff:3.500A) removed outlier: 5.688A pdb=" N TYR D 200 " --> pdb=" O GLY D 169 " (cutoff:3.500A) removed outlier: 6.422A pdb=" N LEU D 199 " --> pdb=" O LEU D 195 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N LEU D 195 " --> pdb=" O LEU D 199 " (cutoff:3.500A) removed outlier: 5.960A pdb=" N THR D 201 " --> pdb=" O ALA D 193 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA D 193 " --> pdb=" O THR D 201 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N SER D 203 " --> pdb=" O PHE D 191 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 176 through 179 439 hydrogen bonds defined for protein. 1251 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: 2.22 Time building geometry restraints manager: 1.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2020 1.34 - 1.46: 1505 1.46 - 1.58: 2742 1.58 - 1.70: 0 1.70 - 1.81: 55 Bond restraints: 6322 Sorted by residual: bond pdb=" CB PRO C 60 " pdb=" CG PRO C 60 " ideal model delta sigma weight residual 1.492 1.558 -0.066 5.00e-02 4.00e+02 1.76e+00 bond pdb=" N GLU D 61 " pdb=" CA GLU D 61 " ideal model delta sigma weight residual 1.457 1.471 -0.014 1.29e-02 6.01e+03 1.18e+00 bond pdb=" CG PRO D 33 " pdb=" CD PRO D 33 " ideal model delta sigma weight residual 1.503 1.539 -0.036 3.40e-02 8.65e+02 1.11e+00 bond pdb=" C ILE A 463 " pdb=" O ILE A 463 " ideal model delta sigma weight residual 1.237 1.248 -0.011 1.13e-02 7.83e+03 9.60e-01 bond pdb=" CB ILE A 467 " pdb=" CG2 ILE A 467 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.23e-01 ... (remaining 6317 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.37: 8413 1.37 - 2.74: 160 2.74 - 4.11: 32 4.11 - 5.49: 14 5.49 - 6.86: 4 Bond angle restraints: 8623 Sorted by residual: angle pdb=" CA PRO C 60 " pdb=" N PRO C 60 " pdb=" CD PRO C 60 " ideal model delta sigma weight residual 112.00 107.19 4.81 1.40e+00 5.10e-01 1.18e+01 angle pdb=" N PRO C 60 " pdb=" CA PRO C 60 " pdb=" C PRO C 60 " ideal model delta sigma weight residual 110.21 113.94 -3.73 1.64e+00 3.72e-01 5.19e+00 angle pdb=" CG ARG A 365 " pdb=" CD ARG A 365 " pdb=" NE ARG A 365 " ideal model delta sigma weight residual 112.00 116.66 -4.66 2.20e+00 2.07e-01 4.48e+00 angle pdb=" N GLU A 290 " pdb=" CA GLU A 290 " pdb=" C GLU A 290 " ideal model delta sigma weight residual 109.81 114.48 -4.67 2.21e+00 2.05e-01 4.46e+00 angle pdb=" CA PRO D 33 " pdb=" N PRO D 33 " pdb=" CD PRO D 33 " ideal model delta sigma weight residual 112.00 109.24 2.76 1.40e+00 5.10e-01 3.89e+00 ... (remaining 8618 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 3202 17.96 - 35.91: 336 35.91 - 53.87: 128 53.87 - 71.83: 10 71.83 - 89.78: 3 Dihedral angle restraints: 3679 sinusoidal: 1170 harmonic: 2509 Sorted by residual: dihedral pdb=" CB CYS A 367 " pdb=" SG CYS A 367 " pdb=" SG CYS A 553 " pdb=" CB CYS A 553 " ideal model delta sinusoidal sigma weight residual -86.00 -113.49 27.49 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" CA ASN A 141 " pdb=" CB ASN A 141 " pdb=" CG ASN A 141 " pdb=" OD1 ASN A 141 " ideal model delta sinusoidal sigma weight residual 120.00 -169.77 -70.23 2 2.00e+01 2.50e-03 1.06e+01 dihedral pdb=" CA ASP D 80 " pdb=" CB ASP D 80 " pdb=" CG ASP D 80 " pdb=" OD1 ASP D 80 " ideal model delta sinusoidal sigma weight residual -30.00 -84.96 54.96 1 2.00e+01 2.50e-03 1.02e+01 ... (remaining 3676 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 605 0.027 - 0.054: 263 0.054 - 0.081: 89 0.081 - 0.108: 52 0.108 - 0.135: 17 Chirality restraints: 1026 Sorted by residual: chirality pdb=" CA GLU A 290 " pdb=" N GLU A 290 " pdb=" C GLU A 290 " pdb=" CB GLU A 290 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.14 2.00e-01 2.50e+01 4.58e-01 chirality pdb=" CB ILE A 467 " pdb=" CA ILE A 467 " pdb=" CG1 ILE A 467 " pdb=" CG2 ILE A 467 " both_signs ideal model delta sigma weight residual False 2.64 2.51 0.13 2.00e-01 2.50e+01 4.33e-01 chirality pdb=" CA ILE C 95 " pdb=" N ILE C 95 " pdb=" C ILE C 95 " pdb=" CB ILE C 95 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.23e-01 ... (remaining 1023 not shown) Planarity restraints: 1095 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ARG D 32 " -0.068 5.00e-02 4.00e+02 1.02e-01 1.67e+01 pdb=" N PRO D 33 " 0.177 5.00e-02 4.00e+02 pdb=" CA PRO D 33 " -0.054 5.00e-02 4.00e+02 pdb=" CD PRO D 33 " -0.055 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 516 " 0.066 5.00e-02 4.00e+02 9.98e-02 1.59e+01 pdb=" N PRO A 517 " -0.173 5.00e-02 4.00e+02 pdb=" CA PRO A 517 " 0.053 5.00e-02 4.00e+02 pdb=" CD PRO A 517 " 0.054 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS C 59 " 0.059 5.00e-02 4.00e+02 8.78e-02 1.23e+01 pdb=" N PRO C 60 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO C 60 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO C 60 " 0.049 5.00e-02 4.00e+02 ... (remaining 1092 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.27: 5 2.27 - 2.93: 2691 2.93 - 3.58: 8950 3.58 - 4.24: 12970 4.24 - 4.90: 22833 Nonbonded interactions: 47449 Sorted by model distance: nonbonded pdb=" SG CYS A 326 " pdb="CO CO A 602 " model vdw 1.612 2.580 nonbonded pdb=" OD2 ASP A 39 " pdb="CO CO A 601 " model vdw 2.026 2.220 nonbonded pdb=" NE2 HIS A 507 " pdb="CO CO A 602 " model vdw 2.130 2.300 nonbonded pdb=" NE2 HIS A 43 " pdb="CO CO A 601 " model vdw 2.145 2.300 nonbonded pdb=" OG SER C 34 " pdb=" OD2 ASP C 37 " model vdw 2.239 3.040 ... (remaining 47444 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: 0.390 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.050 Process input model: 18.340 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.030 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:12.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 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 : 0.003 0.066 6322 Z= 0.176 Angle : 0.534 6.857 8623 Z= 0.285 Chirality : 0.040 0.135 1026 Planarity : 0.007 0.102 1095 Dihedral : 16.820 89.785 2066 Min Nonbonded Distance : 1.612 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.54 % Favored : 97.35 % Rotamer: Outliers : 3.54 % Allowed : 35.40 % Favored : 61.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.02 (0.30), residues: 867 helix: 2.75 (0.25), residues: 402 sheet: 1.13 (0.41), residues: 198 loop : -0.77 (0.38), residues: 267 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP D 69 HIS 0.003 0.001 HIS A 32 PHE 0.009 0.001 PHE C 107 TYR 0.008 0.001 TYR A 64 ARG 0.007 0.001 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 0.661 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8973 (tp) cc_final: 0.8089 (tp) REVERT: D 62 GLN cc_start: 0.8254 (tp40) cc_final: 0.7551 (mp10) outliers start: 20 outliers final: 10 residues processed: 196 average time/residue: 0.9909 time to fit residues: 205.0668 Evaluate side-chains 136 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 126 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 387 CYS Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 103 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 9.9990 chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 43 optimal weight: 6.9990 chunk 34 optimal weight: 0.8980 chunk 67 optimal weight: 0.9990 chunk 26 optimal weight: 7.9990 chunk 40 optimal weight: 8.9990 chunk 50 optimal weight: 9.9990 chunk 78 optimal weight: 50.0000 overall best weight: 2.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 116 HIS A 118 HIS A 182 GLN C 26 GLN C 48 ASN D 22 GLN D 24 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3237 r_free = 0.3237 target = 0.076930 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.057488 restraints weight = 18066.067| |-----------------------------------------------------------------------------| r_work (start): 0.2788 rms_B_bonded: 3.61 r_work: 0.2635 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2635 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.1997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 6322 Z= 0.285 Angle : 0.608 7.580 8623 Z= 0.317 Chirality : 0.042 0.137 1026 Planarity : 0.005 0.067 1095 Dihedral : 5.185 59.650 942 Min Nonbonded Distance : 1.963 Molprobity Statistics. All-atom Clashscore : 6.65 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 8.50 % Allowed : 31.86 % Favored : 59.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.39 (0.30), residues: 867 helix: 2.99 (0.25), residues: 409 sheet: 1.15 (0.38), residues: 206 loop : -0.48 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 37 HIS 0.010 0.002 HIS A 118 PHE 0.013 0.001 PHE C 107 TYR 0.012 0.001 TYR A 538 ARG 0.008 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 48 poor density : 126 time to evaluate : 0.695 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9638 (m) cc_final: 0.9389 (p) REVERT: A 119 GLU cc_start: 0.9151 (tp30) cc_final: 0.8795 (tp30) REVERT: A 166 ASP cc_start: 0.8824 (t0) cc_final: 0.7794 (t0) REVERT: A 219 GLU cc_start: 0.8939 (mt-10) cc_final: 0.8569 (mt-10) REVERT: A 228 GLN cc_start: 0.9367 (OUTLIER) cc_final: 0.9144 (mt0) REVERT: A 324 PHE cc_start: 0.9277 (OUTLIER) cc_final: 0.8094 (t80) REVERT: A 529 SER cc_start: 0.9566 (OUTLIER) cc_final: 0.9350 (p) REVERT: C 38 ARG cc_start: 0.9387 (ptm160) cc_final: 0.9149 (mtp-110) REVERT: C 48 ASN cc_start: 0.9533 (t0) cc_final: 0.9298 (t0) REVERT: C 62 GLN cc_start: 0.8396 (mp10) cc_final: 0.8140 (mp10) REVERT: C 69 TYR cc_start: 0.9468 (p90) cc_final: 0.9172 (p90) REVERT: C 70 SER cc_start: 0.9712 (OUTLIER) cc_final: 0.9052 (p) REVERT: C 101 GLU cc_start: 0.9090 (pm20) cc_final: 0.8832 (pm20) REVERT: D 61 GLU cc_start: 0.8504 (pp20) cc_final: 0.7747 (pp20) REVERT: D 62 GLN cc_start: 0.9270 (tp40) cc_final: 0.8213 (mp10) outliers start: 48 outliers final: 17 residues processed: 160 average time/residue: 1.0158 time to fit residues: 171.9095 Evaluate side-chains 132 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 111 time to evaluate : 0.680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 487 SER Chi-restraints excluded: chain A residue 511 VAL Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 61 optimal weight: 0.9980 chunk 77 optimal weight: 5.9990 chunk 18 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 39 optimal weight: 0.9990 chunk 10 optimal weight: 5.9990 chunk 64 optimal weight: 50.0000 chunk 33 optimal weight: 8.9990 chunk 48 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN D 74 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.076463 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2781 r_free = 0.2781 target = 0.057104 restraints weight = 18305.935| |-----------------------------------------------------------------------------| r_work (start): 0.2756 rms_B_bonded: 3.64 r_work: 0.2600 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2600 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8220 moved from start: 0.2301 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6322 Z= 0.278 Angle : 0.595 7.727 8623 Z= 0.306 Chirality : 0.042 0.150 1026 Planarity : 0.005 0.058 1095 Dihedral : 4.668 59.557 932 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.65 % Favored : 97.23 % Rotamer: Outliers : 7.43 % Allowed : 31.33 % Favored : 61.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.51 (0.30), residues: 867 helix: 3.09 (0.25), residues: 407 sheet: 1.32 (0.39), residues: 201 loop : -0.47 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP D 69 HIS 0.010 0.002 HIS A 118 PHE 0.011 0.001 PHE C 30 TYR 0.011 0.001 TYR C 160 ARG 0.005 0.001 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 114 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9576 (m) cc_final: 0.9337 (p) REVERT: A 119 GLU cc_start: 0.9120 (tp30) cc_final: 0.8802 (tp30) REVERT: A 166 ASP cc_start: 0.8752 (t0) cc_final: 0.7711 (t0) REVERT: A 219 GLU cc_start: 0.8763 (mt-10) cc_final: 0.8507 (mt-10) REVERT: A 228 GLN cc_start: 0.9363 (OUTLIER) cc_final: 0.9113 (mt0) REVERT: A 324 PHE cc_start: 0.9315 (OUTLIER) cc_final: 0.8324 (t80) REVERT: A 364 ARG cc_start: 0.9296 (OUTLIER) cc_final: 0.7561 (ttp-110) REVERT: C 34 SER cc_start: 0.8537 (OUTLIER) cc_final: 0.8325 (p) REVERT: C 39 VAL cc_start: 0.9586 (t) cc_final: 0.9304 (m) REVERT: C 62 GLN cc_start: 0.8294 (mp10) cc_final: 0.8031 (mp10) REVERT: C 69 TYR cc_start: 0.9409 (p90) cc_final: 0.9116 (p90) REVERT: C 70 SER cc_start: 0.9706 (OUTLIER) cc_final: 0.9105 (p) REVERT: C 101 GLU cc_start: 0.9134 (pm20) cc_final: 0.8792 (pm20) outliers start: 42 outliers final: 18 residues processed: 143 average time/residue: 1.1205 time to fit residues: 168.4864 Evaluate side-chains 128 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 105 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 27 optimal weight: 0.0970 chunk 11 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 26 optimal weight: 8.9990 chunk 57 optimal weight: 20.0000 chunk 45 optimal weight: 0.3980 chunk 41 optimal weight: 0.8980 chunk 31 optimal weight: 0.9990 chunk 49 optimal weight: 7.9990 chunk 74 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.078875 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.059591 restraints weight = 18275.232| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.70 r_work: 0.2672 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.038 6322 Z= 0.167 Angle : 0.577 8.927 8623 Z= 0.288 Chirality : 0.041 0.151 1026 Planarity : 0.004 0.057 1095 Dihedral : 4.097 51.080 930 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 5.84 % Allowed : 32.04 % Favored : 62.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.66 (0.30), residues: 867 helix: 3.16 (0.25), residues: 408 sheet: 1.44 (0.38), residues: 205 loop : -0.41 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP D 69 HIS 0.010 0.001 HIS A 118 PHE 0.008 0.001 PHE A 295 TYR 0.007 0.001 TYR A 538 ARG 0.007 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 130 time to evaluate : 0.707 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9572 (m) cc_final: 0.9325 (p) REVERT: A 119 GLU cc_start: 0.9125 (tp30) cc_final: 0.8698 (tm-30) REVERT: A 120 LEU cc_start: 0.9221 (OUTLIER) cc_final: 0.8969 (mm) REVERT: A 127 TRP cc_start: 0.7925 (t60) cc_final: 0.7422 (t-100) REVERT: A 166 ASP cc_start: 0.8554 (t0) cc_final: 0.7947 (t0) REVERT: A 228 GLN cc_start: 0.9336 (OUTLIER) cc_final: 0.9100 (mt0) REVERT: A 324 PHE cc_start: 0.9291 (OUTLIER) cc_final: 0.8657 (t80) REVERT: A 364 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.7236 (ttp-110) REVERT: A 473 ASP cc_start: 0.9647 (t0) cc_final: 0.9417 (t0) REVERT: C 34 SER cc_start: 0.8579 (OUTLIER) cc_final: 0.8202 (p) REVERT: C 39 VAL cc_start: 0.9616 (t) cc_final: 0.9340 (m) REVERT: C 62 GLN cc_start: 0.8455 (mp10) cc_final: 0.8168 (mp10) REVERT: C 70 SER cc_start: 0.9665 (OUTLIER) cc_final: 0.9094 (p) REVERT: C 101 GLU cc_start: 0.9174 (pm20) cc_final: 0.8763 (pm20) REVERT: C 125 GLU cc_start: 0.7789 (tp30) cc_final: 0.7337 (tm-30) REVERT: D 29 GLU cc_start: 0.9326 (mm-30) cc_final: 0.8187 (mp0) outliers start: 33 outliers final: 10 residues processed: 154 average time/residue: 1.0142 time to fit residues: 165.1420 Evaluate side-chains 127 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 111 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 228 GLN Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 34 SER Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 107 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 2 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 53 optimal weight: 6.9990 chunk 6 optimal weight: 0.8980 chunk 34 optimal weight: 0.9980 chunk 76 optimal weight: 7.9990 chunk 63 optimal weight: 40.0000 chunk 52 optimal weight: 4.9990 chunk 60 optimal weight: 8.9990 chunk 45 optimal weight: 6.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN C 48 ASN C 109 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.077884 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2848 r_free = 0.2848 target = 0.059755 restraints weight = 18482.236| |-----------------------------------------------------------------------------| r_work (start): 0.2801 rms_B_bonded: 3.53 r_work: 0.2645 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.2645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6322 Z= 0.257 Angle : 0.608 9.437 8623 Z= 0.305 Chirality : 0.042 0.154 1026 Planarity : 0.004 0.055 1095 Dihedral : 4.035 46.822 930 Min Nonbonded Distance : 1.967 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 6.02 % Allowed : 33.63 % Favored : 60.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.59 (0.30), residues: 867 helix: 3.04 (0.25), residues: 408 sheet: 1.51 (0.38), residues: 201 loop : -0.38 (0.39), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 299 HIS 0.011 0.002 HIS A 118 PHE 0.013 0.001 PHE C 30 TYR 0.010 0.001 TYR C 160 ARG 0.005 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 111 time to evaluate : 0.748 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9598 (m) cc_final: 0.9389 (p) REVERT: A 119 GLU cc_start: 0.9157 (tp30) cc_final: 0.8719 (tm-30) REVERT: A 120 LEU cc_start: 0.9217 (OUTLIER) cc_final: 0.8981 (mm) REVERT: A 127 TRP cc_start: 0.8017 (t60) cc_final: 0.7533 (t-100) REVERT: A 166 ASP cc_start: 0.8732 (t0) cc_final: 0.7626 (t0) REVERT: A 324 PHE cc_start: 0.9330 (OUTLIER) cc_final: 0.8658 (t80) REVERT: A 364 ARG cc_start: 0.9339 (OUTLIER) cc_final: 0.7501 (ttp-110) REVERT: A 473 ASP cc_start: 0.9645 (t0) cc_final: 0.9412 (t0) REVERT: C 38 ARG cc_start: 0.9441 (ptm160) cc_final: 0.9229 (mtp-110) REVERT: C 39 VAL cc_start: 0.9596 (t) cc_final: 0.9292 (m) REVERT: C 62 GLN cc_start: 0.8587 (mp10) cc_final: 0.8306 (mp10) REVERT: C 69 TYR cc_start: 0.9529 (p90) cc_final: 0.9210 (p90) REVERT: C 70 SER cc_start: 0.9735 (OUTLIER) cc_final: 0.9179 (p) REVERT: C 101 GLU cc_start: 0.9225 (pm20) cc_final: 0.8825 (pm20) REVERT: C 125 GLU cc_start: 0.7823 (tp30) cc_final: 0.7398 (tm-30) REVERT: D 61 GLU cc_start: 0.8630 (pp20) cc_final: 0.8140 (pp20) REVERT: D 62 GLN cc_start: 0.9162 (tp40) cc_final: 0.8372 (mp10) REVERT: D 118 LYS cc_start: 0.9256 (OUTLIER) cc_final: 0.8892 (tptp) outliers start: 34 outliers final: 14 residues processed: 137 average time/residue: 1.0736 time to fit residues: 155.0325 Evaluate side-chains 126 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 107 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 533 MET Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 57 optimal weight: 20.0000 chunk 59 optimal weight: 0.9990 chunk 66 optimal weight: 9.9990 chunk 78 optimal weight: 50.0000 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 10.0000 chunk 35 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 82 optimal weight: 6.9990 chunk 55 optimal weight: 20.0000 chunk 5 optimal weight: 0.6980 overall best weight: 2.1504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3229 r_free = 0.3229 target = 0.075964 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2789 r_free = 0.2789 target = 0.057078 restraints weight = 18219.124| |-----------------------------------------------------------------------------| r_work (start): 0.2781 rms_B_bonded: 3.62 r_work: 0.2624 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2624 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8319 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 6322 Z= 0.278 Angle : 0.622 9.294 8623 Z= 0.313 Chirality : 0.042 0.162 1026 Planarity : 0.004 0.053 1095 Dihedral : 3.796 45.540 929 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 6.55 % Allowed : 33.45 % Favored : 60.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 (0.29), residues: 867 helix: 3.03 (0.25), residues: 407 sheet: 1.42 (0.38), residues: 202 loop : -0.38 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 69 HIS 0.011 0.002 HIS A 118 PHE 0.007 0.001 PHE A 324 TYR 0.010 0.001 TYR C 160 ARG 0.003 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 114 time to evaluate : 0.732 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9594 (m) cc_final: 0.9391 (p) REVERT: A 119 GLU cc_start: 0.9148 (tp30) cc_final: 0.8721 (tm-30) REVERT: A 120 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8959 (mm) REVERT: A 127 TRP cc_start: 0.8065 (t60) cc_final: 0.7585 (t-100) REVERT: A 165 GLU cc_start: 0.7456 (mm-30) cc_final: 0.6998 (mm-30) REVERT: A 166 ASP cc_start: 0.8761 (t0) cc_final: 0.7666 (t0) REVERT: A 324 PHE cc_start: 0.9339 (OUTLIER) cc_final: 0.8702 (t80) REVERT: A 338 SER cc_start: 0.7638 (OUTLIER) cc_final: 0.7357 (p) REVERT: A 364 ARG cc_start: 0.9338 (OUTLIER) cc_final: 0.7474 (ttp-110) REVERT: A 473 ASP cc_start: 0.9650 (t0) cc_final: 0.9415 (t0) REVERT: C 38 ARG cc_start: 0.9397 (ptm160) cc_final: 0.9154 (mtp-110) REVERT: C 39 VAL cc_start: 0.9601 (t) cc_final: 0.9305 (m) REVERT: C 62 GLN cc_start: 0.8605 (mp10) cc_final: 0.8288 (mp10) REVERT: C 70 SER cc_start: 0.9732 (OUTLIER) cc_final: 0.9251 (p) REVERT: C 101 GLU cc_start: 0.9209 (pm20) cc_final: 0.8896 (pm20) REVERT: D 118 LYS cc_start: 0.9279 (OUTLIER) cc_final: 0.8905 (tptp) REVERT: D 119 ARG cc_start: 0.8975 (tpt-90) cc_final: 0.8706 (tpt90) outliers start: 37 outliers final: 15 residues processed: 141 average time/residue: 1.0385 time to fit residues: 154.4805 Evaluate side-chains 129 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 108 time to evaluate : 0.683 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 118 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 3.9990 chunk 56 optimal weight: 7.9990 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 chunk 75 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 28 optimal weight: 0.9980 chunk 46 optimal weight: 0.4980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.079443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2858 r_free = 0.2858 target = 0.060116 restraints weight = 18174.020| |-----------------------------------------------------------------------------| r_work (start): 0.2829 rms_B_bonded: 3.68 r_work: 0.2677 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2677 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8201 moved from start: 0.2933 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6322 Z= 0.184 Angle : 0.632 10.454 8623 Z= 0.309 Chirality : 0.042 0.180 1026 Planarity : 0.004 0.054 1095 Dihedral : 3.689 44.882 929 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.77 % Favored : 97.12 % Rotamer: Outliers : 5.66 % Allowed : 35.93 % Favored : 58.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.56 (0.29), residues: 867 helix: 3.04 (0.25), residues: 408 sheet: 1.41 (0.37), residues: 205 loop : -0.39 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP D 69 HIS 0.011 0.001 HIS A 118 PHE 0.008 0.001 PHE A 295 TYR 0.007 0.001 TYR C 111 ARG 0.004 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 132 time to evaluate : 0.731 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9578 (m) cc_final: 0.9344 (p) REVERT: A 119 GLU cc_start: 0.9134 (tp30) cc_final: 0.8715 (tm-30) REVERT: A 120 LEU cc_start: 0.9200 (OUTLIER) cc_final: 0.8976 (mm) REVERT: A 127 TRP cc_start: 0.7948 (t60) cc_final: 0.7475 (t-100) REVERT: A 166 ASP cc_start: 0.8460 (t0) cc_final: 0.7787 (t0) REVERT: A 364 ARG cc_start: 0.9140 (OUTLIER) cc_final: 0.7235 (ttp-110) REVERT: C 39 VAL cc_start: 0.9584 (t) cc_final: 0.9132 (m) REVERT: C 62 GLN cc_start: 0.8592 (mp10) cc_final: 0.8278 (mp10) REVERT: C 69 TYR cc_start: 0.9464 (p90) cc_final: 0.9187 (p90) REVERT: C 70 SER cc_start: 0.9720 (OUTLIER) cc_final: 0.9161 (p) REVERT: C 101 GLU cc_start: 0.9218 (pm20) cc_final: 0.8840 (pm20) REVERT: C 107 PHE cc_start: 0.8957 (p90) cc_final: 0.8685 (p90) REVERT: D 29 GLU cc_start: 0.9300 (mm-30) cc_final: 0.8160 (mp0) REVERT: D 62 GLN cc_start: 0.9150 (tp40) cc_final: 0.8565 (mm-40) REVERT: D 118 LYS cc_start: 0.9160 (OUTLIER) cc_final: 0.8848 (tptp) outliers start: 32 outliers final: 13 residues processed: 153 average time/residue: 0.9822 time to fit residues: 159.0719 Evaluate side-chains 133 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 116 time to evaluate : 0.739 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 198 PHE Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 118 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 2.9990 chunk 80 optimal weight: 8.9990 chunk 22 optimal weight: 9.9990 chunk 1 optimal weight: 4.9990 chunk 79 optimal weight: 6.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 3.9990 chunk 75 optimal weight: 3.9990 chunk 44 optimal weight: 0.0070 chunk 74 optimal weight: 7.9990 chunk 5 optimal weight: 0.9980 overall best weight: 2.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3251 r_free = 0.3251 target = 0.075623 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2811 r_free = 0.2811 target = 0.056441 restraints weight = 18254.603| |-----------------------------------------------------------------------------| r_work (start): 0.2776 rms_B_bonded: 3.60 r_work: 0.2626 rms_B_bonded: 3.99 restraints_weight: 0.5000 r_work (final): 0.2626 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 6322 Z= 0.312 Angle : 0.693 10.553 8623 Z= 0.341 Chirality : 0.044 0.234 1026 Planarity : 0.004 0.053 1095 Dihedral : 3.835 49.066 929 Min Nonbonded Distance : 1.956 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.34 % Favored : 96.54 % Rotamer: Outliers : 6.02 % Allowed : 36.64 % Favored : 57.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.48 (0.29), residues: 867 helix: 2.93 (0.25), residues: 407 sheet: 1.45 (0.38), residues: 202 loop : -0.38 (0.38), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 211 HIS 0.011 0.002 HIS A 118 PHE 0.015 0.001 PHE C 30 TYR 0.010 0.001 TYR C 160 ARG 0.008 0.001 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 146 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 112 time to evaluate : 0.667 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8910 (pt) cc_final: 0.8678 (tm) REVERT: A 102 SER cc_start: 0.9597 (m) cc_final: 0.9393 (p) REVERT: A 119 GLU cc_start: 0.9148 (tp30) cc_final: 0.8758 (tm-30) REVERT: A 120 LEU cc_start: 0.9196 (OUTLIER) cc_final: 0.8949 (mm) REVERT: A 127 TRP cc_start: 0.8104 (t60) cc_final: 0.7615 (t-100) REVERT: A 165 GLU cc_start: 0.8877 (mt-10) cc_final: 0.8648 (mt-10) REVERT: A 166 ASP cc_start: 0.8756 (t0) cc_final: 0.7644 (t0) REVERT: A 338 SER cc_start: 0.7655 (OUTLIER) cc_final: 0.7401 (p) REVERT: A 364 ARG cc_start: 0.9353 (OUTLIER) cc_final: 0.7504 (ttp-110) REVERT: A 529 SER cc_start: 0.9540 (OUTLIER) cc_final: 0.9298 (p) REVERT: C 38 ARG cc_start: 0.9439 (ptm160) cc_final: 0.9203 (mtp-110) REVERT: C 39 VAL cc_start: 0.9545 (t) cc_final: 0.9250 (m) REVERT: C 62 GLN cc_start: 0.8651 (mp10) cc_final: 0.8327 (mp10) REVERT: C 70 SER cc_start: 0.9736 (OUTLIER) cc_final: 0.9264 (p) REVERT: C 101 GLU cc_start: 0.9262 (pm20) cc_final: 0.9013 (pm20) REVERT: D 61 GLU cc_start: 0.8871 (pp20) cc_final: 0.8277 (pp20) REVERT: D 62 GLN cc_start: 0.9236 (tp40) cc_final: 0.8393 (mm-40) outliers start: 34 outliers final: 15 residues processed: 137 average time/residue: 1.0448 time to fit residues: 150.9920 Evaluate side-chains 127 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 107 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 338 SER Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain A residue 529 SER Chi-restraints excluded: chain C residue 25 THR Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 100 SER Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 136 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 42 optimal weight: 0.9980 chunk 27 optimal weight: 4.9990 chunk 13 optimal weight: 0.7980 chunk 46 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 84 optimal weight: 30.0000 chunk 10 optimal weight: 3.9990 chunk 56 optimal weight: 9.9990 chunk 7 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.079473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2882 r_free = 0.2882 target = 0.060506 restraints weight = 18163.211| |-----------------------------------------------------------------------------| r_work (start): 0.2819 rms_B_bonded: 3.63 r_work: 0.2668 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2668 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.3101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6322 Z= 0.209 Angle : 0.710 12.372 8623 Z= 0.335 Chirality : 0.043 0.256 1026 Planarity : 0.004 0.053 1095 Dihedral : 3.750 47.503 929 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 7.41 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 3.72 % Allowed : 38.58 % Favored : 57.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.47 (0.29), residues: 867 helix: 2.91 (0.25), residues: 408 sheet: 1.46 (0.37), residues: 205 loop : -0.40 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 211 HIS 0.012 0.002 HIS A 118 PHE 0.007 0.001 PHE A 295 TYR 0.007 0.001 TYR C 106 ARG 0.006 0.000 ARG C 38 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 122 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9588 (m) cc_final: 0.9358 (p) REVERT: A 119 GLU cc_start: 0.9164 (tp30) cc_final: 0.8739 (tp30) REVERT: A 123 MET cc_start: 0.8788 (tpp) cc_final: 0.8415 (tpt) REVERT: A 127 TRP cc_start: 0.8011 (t60) cc_final: 0.7509 (t-100) REVERT: A 165 GLU cc_start: 0.8886 (mt-10) cc_final: 0.8512 (mt-10) REVERT: A 166 ASP cc_start: 0.8480 (t0) cc_final: 0.7962 (t0) REVERT: A 364 ARG cc_start: 0.9168 (OUTLIER) cc_final: 0.7308 (ttp-110) REVERT: C 38 ARG cc_start: 0.9457 (ptm160) cc_final: 0.9248 (mtp-110) REVERT: C 39 VAL cc_start: 0.9577 (t) cc_final: 0.9288 (m) REVERT: C 62 GLN cc_start: 0.8581 (mp10) cc_final: 0.8250 (mp10) REVERT: C 70 SER cc_start: 0.9734 (OUTLIER) cc_final: 0.9181 (p) REVERT: C 101 GLU cc_start: 0.9236 (pm20) cc_final: 0.8841 (pm20) REVERT: C 109 GLN cc_start: 0.9482 (OUTLIER) cc_final: 0.8798 (tm-30) REVERT: D 31 VAL cc_start: 0.9546 (t) cc_final: 0.9318 (m) REVERT: D 62 GLN cc_start: 0.9178 (tp40) cc_final: 0.8656 (mm-40) outliers start: 21 outliers final: 10 residues processed: 137 average time/residue: 1.0683 time to fit residues: 154.2834 Evaluate side-chains 129 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 116 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 186 ILE Chi-restraints excluded: chain A residue 364 ARG Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 482 GLU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain C residue 109 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 40 optimal weight: 5.9990 chunk 57 optimal weight: 0.6980 chunk 83 optimal weight: 30.0000 chunk 47 optimal weight: 1.9990 chunk 3 optimal weight: 1.9990 chunk 72 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.079775 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.2888 r_free = 0.2888 target = 0.060739 restraints weight = 18459.968| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.65 r_work: 0.2681 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8230 moved from start: 0.3201 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 6322 Z= 0.213 Angle : 0.723 14.619 8623 Z= 0.342 Chirality : 0.043 0.261 1026 Planarity : 0.004 0.053 1095 Dihedral : 3.746 47.513 929 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.58 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 2.83 % Allowed : 40.00 % Favored : 57.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.47 (0.29), residues: 867 helix: 2.89 (0.25), residues: 409 sheet: 1.49 (0.37), residues: 205 loop : -0.40 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 211 HIS 0.013 0.002 HIS A 118 PHE 0.017 0.001 PHE C 30 TYR 0.006 0.001 TYR A 64 ARG 0.006 0.000 ARG C 38 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1734 Ramachandran restraints generated. 867 Oldfield, 0 Emsley, 867 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 118 time to evaluate : 0.718 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.8874 (pt) cc_final: 0.8547 (tm) REVERT: A 102 SER cc_start: 0.9583 (m) cc_final: 0.9355 (p) REVERT: A 119 GLU cc_start: 0.9155 (tp30) cc_final: 0.8700 (tp30) REVERT: A 120 LEU cc_start: 0.9202 (mm) cc_final: 0.8987 (mm) REVERT: A 123 MET cc_start: 0.8813 (tpp) cc_final: 0.8495 (tpt) REVERT: A 127 TRP cc_start: 0.7986 (t60) cc_final: 0.7490 (t-100) REVERT: A 166 ASP cc_start: 0.8521 (t0) cc_final: 0.7416 (t0) REVERT: A 324 PHE cc_start: 0.9263 (OUTLIER) cc_final: 0.8440 (t80) REVERT: C 38 ARG cc_start: 0.9457 (ptm160) cc_final: 0.9251 (mtp-110) REVERT: C 39 VAL cc_start: 0.9583 (t) cc_final: 0.9293 (m) REVERT: C 62 GLN cc_start: 0.8610 (mp10) cc_final: 0.8275 (mp10) REVERT: C 70 SER cc_start: 0.9734 (OUTLIER) cc_final: 0.9183 (p) REVERT: C 101 GLU cc_start: 0.9248 (pm20) cc_final: 0.8860 (pm20) REVERT: D 31 VAL cc_start: 0.9566 (t) cc_final: 0.9346 (m) REVERT: D 42 LYS cc_start: 0.9329 (ttmm) cc_final: 0.8998 (ttpp) REVERT: D 62 GLN cc_start: 0.9145 (tp40) cc_final: 0.8747 (mm-40) outliers start: 16 outliers final: 10 residues processed: 131 average time/residue: 1.1199 time to fit residues: 154.5845 Evaluate side-chains 129 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 117 time to evaluate : 0.702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 53 LEU Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 324 PHE Chi-restraints excluded: chain A residue 378 LEU Chi-restraints excluded: chain A residue 391 VAL Chi-restraints excluded: chain A residue 467 ILE Chi-restraints excluded: chain A residue 469 LEU Chi-restraints excluded: chain A residue 513 LEU Chi-restraints excluded: chain C residue 33 THR Chi-restraints excluded: chain C residue 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 80 optimal weight: 9.9990 chunk 24 optimal weight: 4.9990 chunk 54 optimal weight: 0.8980 chunk 37 optimal weight: 5.9990 chunk 48 optimal weight: 0.9990 chunk 25 optimal weight: 0.4980 chunk 63 optimal weight: 50.0000 chunk 67 optimal weight: 0.7980 chunk 40 optimal weight: 4.9990 chunk 69 optimal weight: 0.2980 chunk 47 optimal weight: 0.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 182 GLN C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.080030 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.060786 restraints weight = 18401.753| |-----------------------------------------------------------------------------| r_work (start): 0.2857 rms_B_bonded: 3.70 r_work: 0.2712 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8241 moved from start: 0.3280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 6322 Z= 0.207 Angle : 0.731 14.225 8623 Z= 0.342 Chirality : 0.043 0.251 1026 Planarity : 0.004 0.053 1095 Dihedral : 3.697 47.297 929 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 2.83 % Allowed : 40.71 % Favored : 56.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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: 2.50 (0.29), residues: 867 helix: 2.91 (0.25), residues: 409 sheet: 1.51 (0.37), residues: 205 loop : -0.40 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 211 HIS 0.014 0.002 HIS A 118 PHE 0.007 0.001 PHE A 295 TYR 0.007 0.001 TYR C 106 ARG 0.006 0.000 ARG C 38 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4071.98 seconds wall clock time: 72 minutes 53.55 seconds (4373.55 seconds total)