Starting phenix.real_space_refine on Tue Mar 3 14:32:26 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8dl8_27499/03_2026/8dl8_27499.cif Found real_map, /net/cci-nas-00/data/ceres_data/8dl8_27499/03_2026/8dl8_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_27499/03_2026/8dl8_27499.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8dl8_27499/03_2026/8dl8_27499.map" model { file = "/net/cci-nas-00/data/ceres_data/8dl8_27499/03_2026/8dl8_27499.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8dl8_27499/03_2026/8dl8_27499.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/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: {'GLU:plan': 7, 'PHE:plan': 3, 'GLN:plan1': 3, 'ASN:plan1': 7, 'ASP:plan': 6, 'TRP:plan': 2, 'ARG:plan': 3, 'TYR:plan': 2, 'HIS:plan': 2} 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: {'TYR:plan': 3, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 2, 'TRP:plan': 2, 'ASN:plan1': 2, 'HIS:plan': 2, 'GLN:plan1': 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: 1.29, per 1000 atoms: 0.21 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: 0.63 Conformation dependent library (CDL) restraints added in 224.2 milliseconds 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: 0.21 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: 1.03 Time building geometry restraints manager: 0.80 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: 0.740 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: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 7.160 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:9.150 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.180 ------------------------------------------------------------------------------- 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 6325 Z= 0.121 Angle : 0.534 6.857 8629 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 : 6.73 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.02 (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 ARG 0.007 0.001 ARG A 365 TYR 0.008 0.001 TYR A 64 PHE 0.009 0.001 PHE C 107 TRP 0.014 0.001 TRP D 69 HIS 0.003 0.001 HIS A 32 Details of bonding type rmsd covalent geometry : bond 0.00259 ( 6322) covalent geometry : angle 0.53427 ( 8623) SS BOND : bond 0.00261 ( 3) SS BOND : angle 0.46258 ( 6) hydrogen bonds : bond 0.12315 ( 439) hydrogen bonds : angle 5.37324 ( 1251) *********************** 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 : 0.260 Fit side-chains revert: symmetry clash REVERT: A 129 LEU cc_start: 0.8973 (tp) cc_final: 0.8078 (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: 0.4461 time to fit residues: 91.9435 Evaluate side-chains 135 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 125 time to evaluate : 0.224 ------------------------------------------------------------------------------- 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 49 optimal weight: 3.9990 chunk 53 optimal weight: 5.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 51 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 61 optimal weight: 20.0000 chunk 45 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- 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 = 0.3204 r_free = 0.3204 target = 0.075345 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2745 r_free = 0.2745 target = 0.055739 restraints weight = 18524.806| |-----------------------------------------------------------------------------| r_work (start): 0.2741 rms_B_bonded: 3.61 r_work: 0.2592 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.2592 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8336 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.039 6325 Z= 0.266 Angle : 0.650 7.588 8629 Z= 0.343 Chirality : 0.043 0.133 1026 Planarity : 0.005 0.070 1095 Dihedral : 5.240 58.731 942 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 7.83 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.23 % Favored : 96.66 % Rotamer: Outliers : 8.85 % Allowed : 31.68 % Favored : 59.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.30), residues: 867 helix: 2.89 (0.25), residues: 409 sheet: 1.11 (0.38), residues: 207 loop : -0.50 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG C 38 TYR 0.014 0.001 TYR C 160 PHE 0.015 0.001 PHE C 107 TRP 0.010 0.001 TRP A 37 HIS 0.010 0.002 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00605 ( 6322) covalent geometry : angle 0.64941 ( 8623) SS BOND : bond 0.00194 ( 3) SS BOND : angle 0.80691 ( 6) hydrogen bonds : bond 0.05867 ( 439) hydrogen bonds : angle 4.57789 ( 1251) *********************** 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 166 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 116 time to evaluate : 0.197 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 99 GLN cc_start: 0.9512 (OUTLIER) cc_final: 0.9204 (tt0) REVERT: A 102 SER cc_start: 0.9618 (m) cc_final: 0.9376 (p) REVERT: A 119 GLU cc_start: 0.9117 (tp30) cc_final: 0.8679 (tp30) REVERT: A 123 MET cc_start: 0.7968 (mmm) cc_final: 0.7620 (mmm) REVERT: A 166 ASP cc_start: 0.8894 (t0) cc_final: 0.7968 (t0) REVERT: A 185 ASN cc_start: 0.9189 (OUTLIER) cc_final: 0.8926 (m-40) REVERT: A 219 GLU cc_start: 0.8929 (mt-10) cc_final: 0.8714 (mt-10) REVERT: C 34 SER cc_start: 0.8944 (OUTLIER) cc_final: 0.8614 (p) REVERT: C 38 ARG cc_start: 0.9381 (ptm160) cc_final: 0.9151 (mtp-110) REVERT: C 48 ASN cc_start: 0.9523 (t0) cc_final: 0.9307 (t0) REVERT: C 62 GLN cc_start: 0.8389 (mp10) cc_final: 0.8141 (mp10) REVERT: C 69 TYR cc_start: 0.9504 (p90) cc_final: 0.9267 (p90) REVERT: C 70 SER cc_start: 0.9712 (OUTLIER) cc_final: 0.9167 (p) REVERT: C 101 GLU cc_start: 0.9109 (pm20) cc_final: 0.8870 (pm20) outliers start: 50 outliers final: 21 residues processed: 153 average time/residue: 0.4556 time to fit residues: 73.3276 Evaluate side-chains 133 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 108 time to evaluate : 0.187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 99 GLN Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 183 LEU Chi-restraints excluded: chain A residue 185 ASN 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 486 GLU 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 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 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 61 GLU Chi-restraints excluded: chain D residue 107 SER 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 70 optimal weight: 0.3980 chunk 30 optimal weight: 0.9980 chunk 54 optimal weight: 9.9990 chunk 31 optimal weight: 0.6980 chunk 27 optimal weight: 0.2980 chunk 79 optimal weight: 50.0000 chunk 12 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 22 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 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 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 = 0.3291 r_free = 0.3291 target = 0.078468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.059601 restraints weight = 18143.947| |-----------------------------------------------------------------------------| r_work (start): 0.2803 rms_B_bonded: 3.62 r_work: 0.2654 rms_B_bonded: 3.96 restraints_weight: 0.5000 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.040 6325 Z= 0.119 Angle : 0.568 7.591 8629 Z= 0.291 Chirality : 0.041 0.150 1026 Planarity : 0.005 0.058 1095 Dihedral : 4.689 60.000 932 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 6.90 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.19 % Favored : 97.69 % Rotamer: Outliers : 7.26 % Allowed : 30.97 % Favored : 61.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.30), residues: 867 helix: 3.14 (0.25), residues: 408 sheet: 1.25 (0.38), residues: 207 loop : -0.52 (0.39), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG D 32 TYR 0.009 0.001 TYR A 538 PHE 0.021 0.001 PHE A 26 TRP 0.009 0.001 TRP D 69 HIS 0.010 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00249 ( 6322) covalent geometry : angle 0.56785 ( 8623) SS BOND : bond 0.00245 ( 3) SS BOND : angle 0.49672 ( 6) hydrogen bonds : bond 0.04634 ( 439) hydrogen bonds : angle 4.08168 ( 1251) *********************** 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 171 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 130 time to evaluate : 0.236 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9180 (tp) cc_final: 0.8968 (tm) REVERT: A 102 SER cc_start: 0.9575 (m) cc_final: 0.9330 (p) REVERT: A 119 GLU cc_start: 0.9146 (tp30) cc_final: 0.8780 (tm-30) REVERT: A 166 ASP cc_start: 0.8646 (t0) cc_final: 0.7501 (t0) REVERT: A 185 ASN cc_start: 0.9122 (OUTLIER) cc_final: 0.8921 (m-40) REVERT: A 211 TRP cc_start: 0.9227 (t-100) cc_final: 0.9012 (t-100) REVERT: A 219 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8584 (mt-10) REVERT: A 312 MET cc_start: 0.9333 (tpp) cc_final: 0.9097 (mmm) REVERT: A 324 PHE cc_start: 0.9200 (OUTLIER) cc_final: 0.8279 (t80) REVERT: A 364 ARG cc_start: 0.9211 (OUTLIER) cc_final: 0.7433 (ttp-110) REVERT: C 39 VAL cc_start: 0.9610 (t) cc_final: 0.9347 (m) REVERT: C 48 ASN cc_start: 0.9522 (t0) cc_final: 0.9317 (t0) REVERT: C 62 GLN cc_start: 0.8317 (mp10) cc_final: 0.8048 (mp10) REVERT: C 69 TYR cc_start: 0.9423 (p90) cc_final: 0.9175 (p90) REVERT: C 70 SER cc_start: 0.9657 (OUTLIER) cc_final: 0.8956 (p) REVERT: C 101 GLU cc_start: 0.9139 (pm20) cc_final: 0.8779 (pm20) REVERT: C 125 GLU cc_start: 0.7665 (tp30) cc_final: 0.7284 (tm-30) REVERT: D 29 GLU cc_start: 0.9370 (mm-30) cc_final: 0.8432 (mp0) REVERT: D 61 GLU cc_start: 0.8629 (pp20) cc_final: 0.8140 (pp20) REVERT: D 62 GLN cc_start: 0.9261 (tp40) cc_final: 0.8375 (mm-40) REVERT: D 65 GLU cc_start: 0.9099 (OUTLIER) cc_final: 0.8743 (mp0) outliers start: 41 outliers final: 14 residues processed: 153 average time/residue: 0.4704 time to fit residues: 75.7310 Evaluate side-chains 133 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 114 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 48 VAL Chi-restraints excluded: chain A residue 120 LEU Chi-restraints excluded: chain A residue 185 ASN Chi-restraints excluded: chain A residue 186 ILE 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 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 100 SER Chi-restraints excluded: chain D residue 36 LEU Chi-restraints excluded: chain D residue 44 SER Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 65 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 66 optimal weight: 9.9990 chunk 14 optimal weight: 0.6980 chunk 77 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 59 optimal weight: 40.0000 chunk 49 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 52 optimal weight: 4.9990 overall best weight: 1.4384 ------------------------------------------------------------------------------- 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 = 0.3275 r_free = 0.3275 target = 0.076938 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2845 r_free = 0.2845 target = 0.057960 restraints weight = 18355.439| |-----------------------------------------------------------------------------| r_work (start): 0.2817 rms_B_bonded: 3.65 r_work: 0.2664 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.2664 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.2404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6325 Z= 0.140 Angle : 0.576 8.309 8629 Z= 0.290 Chirality : 0.041 0.148 1026 Planarity : 0.004 0.057 1095 Dihedral : 4.076 52.418 929 Min Nonbonded Distance : 1.991 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 6.19 % Allowed : 33.10 % Favored : 60.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.61 (0.30), residues: 867 helix: 3.15 (0.25), residues: 407 sheet: 1.42 (0.38), residues: 201 loop : -0.43 (0.38), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG C 38 TYR 0.008 0.001 TYR C 160 PHE 0.011 0.001 PHE C 30 TRP 0.008 0.001 TRP D 69 HIS 0.010 0.002 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00315 ( 6322) covalent geometry : angle 0.57571 ( 8623) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.58572 ( 6) hydrogen bonds : bond 0.04628 ( 439) hydrogen bonds : angle 4.04386 ( 1251) *********************** 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 153 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 118 time to evaluate : 0.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LEU cc_start: 0.9154 (tp) cc_final: 0.8882 (tm) REVERT: A 102 SER cc_start: 0.9587 (m) cc_final: 0.9357 (p) REVERT: A 119 GLU cc_start: 0.9112 (tp30) cc_final: 0.8753 (tm-30) REVERT: A 166 ASP cc_start: 0.8710 (t0) cc_final: 0.7585 (t0) REVERT: A 219 GLU cc_start: 0.8863 (mt-10) cc_final: 0.8538 (mt-10) REVERT: A 324 PHE cc_start: 0.9275 (OUTLIER) cc_final: 0.8421 (t80) REVERT: A 473 ASP cc_start: 0.9649 (t0) cc_final: 0.9411 (t0) REVERT: C 34 SER cc_start: 0.8691 (OUTLIER) cc_final: 0.8415 (p) REVERT: C 39 VAL cc_start: 0.9630 (t) cc_final: 0.9361 (m) REVERT: C 62 GLN cc_start: 0.8445 (mp10) cc_final: 0.8174 (mp10) REVERT: C 70 SER cc_start: 0.9667 (OUTLIER) cc_final: 0.9105 (p) REVERT: C 101 GLU cc_start: 0.9187 (pm20) cc_final: 0.8823 (pm20) REVERT: C 125 GLU cc_start: 0.7819 (tp30) cc_final: 0.7411 (tm-30) REVERT: D 29 GLU cc_start: 0.9353 (mm-30) cc_final: 0.8271 (mp0) outliers start: 35 outliers final: 13 residues processed: 142 average time/residue: 0.4444 time to fit residues: 66.4627 Evaluate side-chains 125 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 109 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 186 ILE 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 512 ILE Chi-restraints excluded: chain A residue 513 LEU 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 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 211 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 41 optimal weight: 0.3980 chunk 65 optimal weight: 0.9990 chunk 70 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.0980 chunk 73 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 9.9990 chunk 21 optimal weight: 3.9990 chunk 44 optimal weight: 0.6980 overall best weight: 0.6382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS A 141 ASN A 182 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.079358 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2856 r_free = 0.2856 target = 0.060237 restraints weight = 18421.444| |-----------------------------------------------------------------------------| r_work (start): 0.2826 rms_B_bonded: 3.73 r_work: 0.2675 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2675 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8178 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 6325 Z= 0.113 Angle : 0.587 9.602 8629 Z= 0.289 Chirality : 0.041 0.147 1026 Planarity : 0.004 0.054 1095 Dihedral : 3.949 45.607 929 Min Nonbonded Distance : 2.044 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.65 % Favored : 97.23 % Rotamer: Outliers : 4.96 % Allowed : 34.34 % Favored : 60.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.68 (0.30), residues: 867 helix: 3.13 (0.25), residues: 408 sheet: 1.51 (0.38), residues: 205 loop : -0.34 (0.39), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG C 38 TYR 0.007 0.001 TYR A 64 PHE 0.008 0.001 PHE A 295 TRP 0.008 0.001 TRP D 69 HIS 0.011 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 6322) covalent geometry : angle 0.58662 ( 8623) SS BOND : bond 0.00247 ( 3) SS BOND : angle 0.55173 ( 6) hydrogen bonds : bond 0.04131 ( 439) hydrogen bonds : angle 3.90097 ( 1251) *********************** 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 153 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 125 time to evaluate : 0.172 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9573 (m) cc_final: 0.9302 (p) REVERT: A 119 GLU cc_start: 0.9116 (tp30) cc_final: 0.8706 (tm-30) REVERT: A 120 LEU cc_start: 0.9284 (OUTLIER) cc_final: 0.9012 (mm) REVERT: A 127 TRP cc_start: 0.7915 (t60) cc_final: 0.7440 (t-100) REVERT: A 166 ASP cc_start: 0.8483 (t0) cc_final: 0.7839 (t0) REVERT: A 219 GLU cc_start: 0.8847 (mt-10) cc_final: 0.8538 (mt-10) REVERT: A 324 PHE cc_start: 0.9262 (OUTLIER) cc_final: 0.8628 (t80) REVERT: A 473 ASP cc_start: 0.9646 (t0) cc_final: 0.9397 (t0) REVERT: C 38 ARG cc_start: 0.9466 (ptm160) cc_final: 0.9251 (mtp-110) REVERT: C 39 VAL cc_start: 0.9625 (t) cc_final: 0.9316 (m) REVERT: C 62 GLN cc_start: 0.8466 (mp10) cc_final: 0.8194 (mp10) REVERT: C 70 SER cc_start: 0.9653 (OUTLIER) cc_final: 0.9048 (p) REVERT: C 101 GLU cc_start: 0.9193 (pm20) cc_final: 0.8789 (pm20) REVERT: C 125 GLU cc_start: 0.7851 (tp30) cc_final: 0.7452 (tm-30) REVERT: D 29 GLU cc_start: 0.9279 (mm-30) cc_final: 0.8129 (mp0) REVERT: D 62 GLN cc_start: 0.9131 (tp40) cc_final: 0.8449 (mm-40) REVERT: D 118 LYS cc_start: 0.9128 (OUTLIER) cc_final: 0.8849 (tptp) outliers start: 28 outliers final: 7 residues processed: 147 average time/residue: 0.4533 time to fit residues: 70.1714 Evaluate side-chains 123 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 112 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 378 LEU 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 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR 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 7 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 chunk 22 optimal weight: 6.9990 chunk 63 optimal weight: 50.0000 chunk 67 optimal weight: 5.9990 chunk 29 optimal weight: 2.9990 chunk 3 optimal weight: 0.9980 chunk 71 optimal weight: 0.8980 chunk 80 optimal weight: 9.9990 chunk 85 optimal weight: 20.0000 chunk 74 optimal weight: 6.9990 overall best weight: 3.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 118 HIS C 48 ASN ** C 109 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.075046 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.055897 restraints weight = 18585.121| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 3.61 r_work: 0.2597 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.2597 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.2890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.051 6325 Z= 0.249 Angle : 0.683 9.372 8629 Z= 0.343 Chirality : 0.043 0.156 1026 Planarity : 0.004 0.054 1095 Dihedral : 3.881 46.905 928 Min Nonbonded Distance : 1.932 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 7.26 % Allowed : 32.92 % Favored : 59.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.46 (0.29), residues: 867 helix: 2.89 (0.25), residues: 409 sheet: 1.42 (0.38), residues: 202 loop : -0.34 (0.38), residues: 256 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG C 38 TYR 0.015 0.001 TYR C 160 PHE 0.013 0.001 PHE C 30 TRP 0.009 0.001 TRP A 224 HIS 0.011 0.002 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00572 ( 6322) covalent geometry : angle 0.68247 ( 8623) SS BOND : bond 0.00149 ( 3) SS BOND : angle 0.77502 ( 6) hydrogen bonds : bond 0.05808 ( 439) hydrogen bonds : angle 4.33618 ( 1251) *********************** 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 146 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 105 time to evaluate : 0.216 Fit side-chains revert: symmetry clash REVERT: A 102 SER cc_start: 0.9591 (m) cc_final: 0.9385 (p) REVERT: A 119 GLU cc_start: 0.9112 (tp30) cc_final: 0.8682 (tm-30) REVERT: A 166 ASP cc_start: 0.8918 (t0) cc_final: 0.7936 (t0) REVERT: A 185 ASN cc_start: 0.9289 (OUTLIER) cc_final: 0.9035 (m-40) REVERT: A 219 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8650 (mt-10) REVERT: A 324 PHE cc_start: 0.9359 (OUTLIER) cc_final: 0.8539 (t80) REVERT: A 473 ASP cc_start: 0.9656 (t0) cc_final: 0.9410 (t0) REVERT: C 39 VAL cc_start: 0.9619 (t) cc_final: 0.9320 (m) REVERT: C 62 GLN cc_start: 0.8593 (mp10) cc_final: 0.8328 (mp10) REVERT: C 69 TYR cc_start: 0.9521 (p90) cc_final: 0.9289 (p90) REVERT: C 70 SER cc_start: 0.9715 (OUTLIER) cc_final: 0.9243 (p) REVERT: C 101 GLU cc_start: 0.9211 (pm20) cc_final: 0.8847 (pm20) REVERT: D 42 LYS cc_start: 0.9378 (ttmm) cc_final: 0.9114 (ttpp) REVERT: D 62 GLN cc_start: 0.9174 (tp40) cc_final: 0.8488 (mm-40) outliers start: 41 outliers final: 14 residues processed: 135 average time/residue: 0.4867 time to fit residues: 69.0079 Evaluate side-chains 118 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 101 time to evaluate : 0.179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 123 MET Chi-restraints excluded: chain A residue 185 ASN 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 487 SER Chi-restraints excluded: chain A residue 513 LEU 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 211 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 82 optimal weight: 30.0000 chunk 15 optimal weight: 5.9990 chunk 25 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 4.9990 chunk 36 optimal weight: 0.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- 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 C 109 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.078081 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2821 r_free = 0.2821 target = 0.058837 restraints weight = 18445.395| |-----------------------------------------------------------------------------| r_work (start): 0.2793 rms_B_bonded: 3.71 r_work: 0.2640 rms_B_bonded: 4.08 restraints_weight: 0.5000 r_work (final): 0.2640 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.2925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6325 Z= 0.138 Angle : 0.674 10.841 8629 Z= 0.322 Chirality : 0.042 0.155 1026 Planarity : 0.004 0.053 1095 Dihedral : 3.746 44.700 928 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 7.66 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.11 % Favored : 96.77 % Rotamer: Outliers : 5.13 % Allowed : 36.11 % Favored : 58.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.54 (0.29), residues: 867 helix: 3.04 (0.26), residues: 407 sheet: 1.36 (0.37), residues: 207 loop : -0.37 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG C 38 TYR 0.010 0.001 TYR A 501 PHE 0.008 0.001 PHE A 324 TRP 0.009 0.001 TRP D 69 HIS 0.010 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 6322) covalent geometry : angle 0.67404 ( 8623) SS BOND : bond 0.00204 ( 3) SS BOND : angle 0.53244 ( 6) hydrogen bonds : bond 0.04573 ( 439) hydrogen bonds : angle 4.00113 ( 1251) *********************** 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 148 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 119 time to evaluate : 0.166 Fit side-chains revert: symmetry clash REVERT: A 102 SER cc_start: 0.9594 (m) cc_final: 0.9381 (p) REVERT: A 119 GLU cc_start: 0.9132 (tp30) cc_final: 0.8693 (tm-30) REVERT: A 120 LEU cc_start: 0.9266 (OUTLIER) cc_final: 0.8965 (mm) REVERT: A 165 GLU cc_start: 0.7804 (mm-30) cc_final: 0.6763 (mm-30) REVERT: A 166 ASP cc_start: 0.8669 (t0) cc_final: 0.7550 (t0) REVERT: A 196 MET cc_start: 0.9364 (tpp) cc_final: 0.9125 (tpt) REVERT: A 219 GLU cc_start: 0.8880 (mt-10) cc_final: 0.8505 (mt-10) REVERT: A 324 PHE cc_start: 0.9311 (OUTLIER) cc_final: 0.8739 (t80) REVERT: A 364 ARG cc_start: 0.9213 (OUTLIER) cc_final: 0.7267 (ttp-110) REVERT: C 39 VAL cc_start: 0.9571 (t) cc_final: 0.9293 (m) REVERT: C 62 GLN cc_start: 0.8568 (mp10) cc_final: 0.8235 (mp10) REVERT: C 69 TYR cc_start: 0.9478 (p90) cc_final: 0.9235 (p90) REVERT: C 70 SER cc_start: 0.9705 (OUTLIER) cc_final: 0.9150 (p) REVERT: C 101 GLU cc_start: 0.9241 (pm20) cc_final: 0.8877 (pm20) REVERT: D 42 LYS cc_start: 0.9325 (ttmm) cc_final: 0.8994 (ttpp) REVERT: D 61 GLU cc_start: 0.8573 (pp20) cc_final: 0.7912 (pp20) REVERT: D 62 GLN cc_start: 0.9175 (tp40) cc_final: 0.8313 (mp10) REVERT: D 119 ARG cc_start: 0.9006 (tpt-90) cc_final: 0.8679 (tpp80) outliers start: 29 outliers final: 10 residues processed: 141 average time/residue: 0.4726 time to fit residues: 70.0527 Evaluate side-chains 124 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 110 time to evaluate : 0.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 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 513 LEU 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 D residue 57 LYS Chi-restraints excluded: chain D residue 211 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 72 optimal weight: 4.9990 chunk 16 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 78 optimal weight: 40.0000 chunk 74 optimal weight: 1.9990 chunk 4 optimal weight: 0.5980 chunk 76 optimal weight: 0.8980 chunk 48 optimal weight: 0.9980 chunk 14 optimal weight: 2.9990 chunk 82 optimal weight: 20.0000 chunk 12 optimal weight: 0.9980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 = 0.3283 r_free = 0.3283 target = 0.078801 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2850 r_free = 0.2850 target = 0.059655 restraints weight = 18225.975| |-----------------------------------------------------------------------------| r_work (start): 0.2822 rms_B_bonded: 3.70 r_work: 0.2672 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2672 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 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 : 0.003 0.036 6325 Z= 0.128 Angle : 0.684 13.669 8629 Z= 0.324 Chirality : 0.042 0.159 1026 Planarity : 0.004 0.053 1095 Dihedral : 3.705 44.946 928 Min Nonbonded Distance : 2.026 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 2.88 % Favored : 97.00 % Rotamer: Outliers : 4.42 % Allowed : 37.17 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.53 (0.29), residues: 867 helix: 3.01 (0.25), residues: 407 sheet: 1.36 (0.37), residues: 206 loop : -0.36 (0.38), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 38 TYR 0.007 0.001 TYR C 111 PHE 0.015 0.001 PHE C 30 TRP 0.010 0.001 TRP D 69 HIS 0.012 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00291 ( 6322) covalent geometry : angle 0.68404 ( 8623) SS BOND : bond 0.00187 ( 3) SS BOND : angle 0.49332 ( 6) hydrogen bonds : bond 0.04310 ( 439) hydrogen bonds : angle 3.91546 ( 1251) *********************** 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 145 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 120 time to evaluate : 0.278 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9584 (m) cc_final: 0.9354 (p) REVERT: A 119 GLU cc_start: 0.9124 (tp30) cc_final: 0.8663 (tm-30) REVERT: A 120 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.8939 (mm) REVERT: A 166 ASP cc_start: 0.8528 (t0) cc_final: 0.7970 (t0) REVERT: A 219 GLU cc_start: 0.8826 (mt-10) cc_final: 0.8540 (mt-10) REVERT: A 324 PHE cc_start: 0.9300 (OUTLIER) cc_final: 0.8796 (t80) REVERT: C 37 ASP cc_start: 0.8513 (m-30) cc_final: 0.8308 (p0) REVERT: C 39 VAL cc_start: 0.9602 (t) cc_final: 0.9144 (m) REVERT: C 62 GLN cc_start: 0.8579 (mp10) cc_final: 0.8268 (mp10) REVERT: C 70 SER cc_start: 0.9681 (OUTLIER) cc_final: 0.9117 (p) REVERT: C 101 GLU cc_start: 0.9240 (pm20) cc_final: 0.8877 (pm20) REVERT: D 42 LYS cc_start: 0.9245 (ttmm) cc_final: 0.8922 (ttpp) REVERT: D 61 GLU cc_start: 0.8513 (pp20) cc_final: 0.8066 (OUTLIER) REVERT: D 62 GLN cc_start: 0.9228 (tp40) cc_final: 0.8450 (mm-40) outliers start: 25 outliers final: 14 residues processed: 139 average time/residue: 0.4615 time to fit residues: 67.5305 Evaluate side-chains 130 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 114 time to evaluate : 0.217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 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 482 GLU Chi-restraints excluded: chain A residue 507 HIS Chi-restraints excluded: chain A residue 512 ILE Chi-restraints excluded: chain A residue 513 LEU 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 D residue 57 LYS Chi-restraints excluded: chain D residue 107 SER Chi-restraints excluded: chain D residue 211 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 49 optimal weight: 0.0050 chunk 17 optimal weight: 0.9980 chunk 3 optimal weight: 0.9990 chunk 55 optimal weight: 50.0000 chunk 44 optimal weight: 0.0020 chunk 83 optimal weight: 30.0000 chunk 42 optimal weight: 4.9990 chunk 65 optimal weight: 2.9990 chunk 53 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 overall best weight: 0.8006 ------------------------------------------------------------------------------- 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 = 0.3302 r_free = 0.3302 target = 0.079755 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2875 r_free = 0.2875 target = 0.060547 restraints weight = 18239.876| |-----------------------------------------------------------------------------| r_work (start): 0.2840 rms_B_bonded: 3.74 r_work: 0.2688 rms_B_bonded: 4.10 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8173 moved from start: 0.3121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 6325 Z= 0.130 Angle : 0.706 11.913 8629 Z= 0.333 Chirality : 0.043 0.167 1026 Planarity : 0.004 0.055 1095 Dihedral : 3.693 44.657 928 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 4.07 % Allowed : 37.70 % Favored : 58.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.29), residues: 867 helix: 2.93 (0.25), residues: 408 sheet: 1.40 (0.37), residues: 206 loop : -0.39 (0.38), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG C 38 TYR 0.006 0.001 TYR C 111 PHE 0.008 0.001 PHE A 295 TRP 0.010 0.001 TRP D 69 HIS 0.012 0.001 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00298 ( 6322) covalent geometry : angle 0.70643 ( 8623) SS BOND : bond 0.00193 ( 3) SS BOND : angle 0.46156 ( 6) hydrogen bonds : bond 0.04250 ( 439) hydrogen bonds : angle 3.92971 ( 1251) *********************** 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 139 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 116 time to evaluate : 0.221 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 102 SER cc_start: 0.9571 (m) cc_final: 0.9335 (p) REVERT: A 119 GLU cc_start: 0.9121 (tp30) cc_final: 0.8677 (tm-30) REVERT: A 120 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8954 (mm) REVERT: A 166 ASP cc_start: 0.8480 (t0) cc_final: 0.7845 (t0) REVERT: A 219 GLU cc_start: 0.8809 (mt-10) cc_final: 0.8571 (mt-10) REVERT: A 364 ARG cc_start: 0.9107 (OUTLIER) cc_final: 0.7188 (ttp-110) REVERT: C 39 VAL cc_start: 0.9624 (t) cc_final: 0.9180 (m) REVERT: C 62 GLN cc_start: 0.8533 (mp10) cc_final: 0.8220 (mp10) REVERT: C 69 TYR cc_start: 0.9397 (p90) cc_final: 0.9131 (p90) REVERT: C 70 SER cc_start: 0.9651 (OUTLIER) cc_final: 0.9091 (p) REVERT: C 101 GLU cc_start: 0.9222 (pm20) cc_final: 0.8840 (pm20) REVERT: D 42 LYS cc_start: 0.9222 (ttmm) cc_final: 0.8903 (ttpp) REVERT: D 61 GLU cc_start: 0.8477 (pp20) cc_final: 0.8225 (OUTLIER) REVERT: D 62 GLN cc_start: 0.9181 (tp40) cc_final: 0.8500 (mm-40) outliers start: 23 outliers final: 12 residues processed: 132 average time/residue: 0.5036 time to fit residues: 69.6663 Evaluate side-chains 126 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 112 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 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 512 ILE Chi-restraints excluded: chain A residue 513 LEU 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 D residue 57 LYS Chi-restraints excluded: chain D residue 211 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 25 optimal weight: 0.9990 chunk 37 optimal weight: 3.9990 chunk 59 optimal weight: 7.9990 chunk 68 optimal weight: 5.9990 chunk 4 optimal weight: 7.9990 chunk 57 optimal weight: 20.0000 chunk 27 optimal weight: 3.9990 chunk 60 optimal weight: 20.0000 chunk 75 optimal weight: 2.9990 chunk 51 optimal weight: 10.0000 chunk 63 optimal weight: 40.0000 overall best weight: 3.5990 ------------------------------------------------------------------------------- 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 = 0.3214 r_free = 0.3214 target = 0.073807 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2761 r_free = 0.2761 target = 0.054408 restraints weight = 18544.590| |-----------------------------------------------------------------------------| r_work (start): 0.2738 rms_B_bonded: 3.63 r_work: 0.2582 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.2582 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.055 6325 Z= 0.280 Angle : 0.775 13.937 8629 Z= 0.382 Chirality : 0.044 0.148 1026 Planarity : 0.004 0.052 1095 Dihedral : 3.908 45.167 928 Min Nonbonded Distance : 1.929 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.46 % Favored : 96.42 % Rotamer: Outliers : 3.36 % Allowed : 38.76 % Favored : 57.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.29 (0.29), residues: 867 helix: 2.77 (0.25), residues: 408 sheet: 1.26 (0.37), residues: 208 loop : -0.42 (0.38), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG C 38 TYR 0.015 0.001 TYR C 160 PHE 0.014 0.001 PHE C 30 TRP 0.012 0.002 TRP A 42 HIS 0.012 0.002 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00642 ( 6322) covalent geometry : angle 0.77511 ( 8623) SS BOND : bond 0.00201 ( 3) SS BOND : angle 0.71894 ( 6) hydrogen bonds : bond 0.05900 ( 439) hydrogen bonds : angle 4.39762 ( 1251) ********************** 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 124 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 105 time to evaluate : 0.175 Fit side-chains revert: symmetry clash REVERT: A 119 GLU cc_start: 0.9114 (tp30) cc_final: 0.8617 (tm-30) REVERT: A 120 LEU cc_start: 0.9259 (OUTLIER) cc_final: 0.8932 (mm) REVERT: A 165 GLU cc_start: 0.7851 (mm-30) cc_final: 0.7136 (mm-30) REVERT: A 166 ASP cc_start: 0.8949 (t0) cc_final: 0.7903 (t0) REVERT: C 38 ARG cc_start: 0.9506 (ptm160) cc_final: 0.9293 (mtp-110) REVERT: C 39 VAL cc_start: 0.9586 (t) cc_final: 0.9251 (m) REVERT: C 62 GLN cc_start: 0.8625 (mp10) cc_final: 0.8259 (mp10) REVERT: C 70 SER cc_start: 0.9713 (OUTLIER) cc_final: 0.9258 (p) REVERT: C 101 GLU cc_start: 0.9269 (pm20) cc_final: 0.8927 (pm20) REVERT: D 37 VAL cc_start: 0.9308 (t) cc_final: 0.9041 (p) REVERT: D 61 GLU cc_start: 0.8659 (pp20) cc_final: 0.8434 (OUTLIER) REVERT: D 62 GLN cc_start: 0.9240 (tp40) cc_final: 0.8559 (mm-40) REVERT: D 119 ARG cc_start: 0.9143 (tpt-90) cc_final: 0.8846 (tpp80) outliers start: 19 outliers final: 10 residues processed: 119 average time/residue: 0.5004 time to fit residues: 62.3497 Evaluate side-chains 112 residues out of total 743 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 101 time to evaluate : 0.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 120 LEU 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 70 SER Chi-restraints excluded: chain C residue 83 THR Chi-restraints excluded: chain C residue 92 THR Chi-restraints excluded: chain D residue 57 LYS Chi-restraints excluded: chain D residue 211 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 86 random chunks: chunk 54 optimal weight: 3.9990 chunk 55 optimal weight: 50.0000 chunk 23 optimal weight: 0.3980 chunk 59 optimal weight: 50.0000 chunk 76 optimal weight: 1.9990 chunk 26 optimal weight: 0.0170 chunk 69 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 79 optimal weight: 40.0000 chunk 70 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7000 ------------------------------------------------------------------------------- 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 = 0.3281 r_free = 0.3281 target = 0.078539 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2861 r_free = 0.2861 target = 0.059783 restraints weight = 18176.213| |-----------------------------------------------------------------------------| r_work (start): 0.2830 rms_B_bonded: 3.67 r_work: 0.2681 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8205 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6325 Z= 0.129 Angle : 0.732 13.599 8629 Z= 0.343 Chirality : 0.043 0.161 1026 Planarity : 0.004 0.052 1095 Dihedral : 3.724 44.034 928 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.12 % Allowed : 3.00 % Favored : 96.89 % Rotamer: Outliers : 3.19 % Allowed : 39.29 % Favored : 57.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.42 (0.29), residues: 867 helix: 2.93 (0.25), residues: 408 sheet: 1.28 (0.37), residues: 208 loop : -0.41 (0.39), residues: 251 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG C 38 TYR 0.008 0.001 TYR A 64 PHE 0.007 0.001 PHE A 324 TRP 0.011 0.001 TRP D 69 HIS 0.012 0.002 HIS A 118 Details of bonding type rmsd covalent geometry : bond 0.00293 ( 6322) covalent geometry : angle 0.73209 ( 8623) SS BOND : bond 0.00243 ( 3) SS BOND : angle 0.46182 ( 6) hydrogen bonds : bond 0.04270 ( 439) hydrogen bonds : angle 3.98320 ( 1251) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1977.07 seconds wall clock time: 34 minutes 24.66 seconds (2064.66 seconds total)