Starting phenix.real_space_refine on Tue Aug 4 12:26:36 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9v3c_64752/08_2026/9v3c_64752.cif Found real_map, /net/cci-nas-00/data/ceres_data/9v3c_64752/08_2026/9v3c_64752.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9v3c_64752/08_2026/9v3c_64752.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9v3c_64752/08_2026/9v3c_64752.map" model { file = "/net/cci-nas-00/data/ceres_data/9v3c_64752/08_2026/9v3c_64752.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9v3c_64752/08_2026/9v3c_64752.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.012 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 25 5.16 5 C 1680 2.51 5 N 456 2.21 5 O 437 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2598 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2115 Number of conformers: 1 Conformer: "" Number of residues, atoms: 286, 2115 Classifications: {'peptide': 286} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 17, 'TRANS': 267} Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "D" Number of atoms: 483 Number of conformers: 1 Conformer: "" Number of residues, atoms: 74, 483 Classifications: {'peptide': 74} Modifications used: {'COO': 1} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 22} Link IDs: {'PTRANS': 1, 'TRANS': 72} Unresolved non-hydrogen bonds: 92 Unresolved non-hydrogen angles: 112 Unresolved non-hydrogen dihedrals: 77 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'GLN:plan1': 2, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 51 Time building chain proxies: 0.63, per 1000 atoms: 0.24 Number of scatterers: 2598 At special positions: 0 Unit cell: (49.8, 64.74, 102.09, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 25 16.00 O 437 8.00 N 456 7.00 C 1680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS A 107 " - pdb=" SG CYS A 186 " distance=2.03 Simple disulfide: pdb=" SG CYS A 133 " - pdb=" SG CYS A 219 " distance=2.03 Simple disulfide: pdb=" SG CYS D 21 " - pdb=" SG CYS D 47 " distance=2.04 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 54 " distance=2.04 Simple disulfide: pdb=" SG CYS D 34 " - pdb=" SG CYS D 55 " 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: 0.14 Conformation dependent library (CDL) restraints added in 67.2 milliseconds 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 670 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 2 sheets defined 80.0% alpha, 1.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 31 through 36 Processing helix chain 'A' and resid 37 through 64 removed outlier: 3.757A pdb=" N LEU A 41 " --> pdb=" O ALA A 37 " (cutoff:3.500A) Proline residue: A 51 - end of helix Processing helix chain 'A' and resid 69 through 96 removed outlier: 4.083A pdb=" N LEU A 73 " --> pdb=" O GLY A 69 " (cutoff:3.500A) Proline residue: A 88 - end of helix Proline residue: A 93 - end of helix Processing helix chain 'A' and resid 102 through 137 Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 139 through 143 Processing helix chain 'A' and resid 146 through 167 removed outlier: 4.259A pdb=" N GLN A 152 " --> pdb=" O ALA A 148 " (cutoff:3.500A) Processing helix chain 'A' and resid 167 through 172 removed outlier: 3.807A pdb=" N TYR A 172 " --> pdb=" O PRO A 168 " (cutoff:3.500A) Processing helix chain 'A' and resid 193 through 209 Processing helix chain 'A' and resid 209 through 226 removed outlier: 4.212A pdb=" N LEU A 224 " --> pdb=" O HIS A 220 " (cutoff:3.500A) Processing helix chain 'A' and resid 232 through 259 removed outlier: 3.940A pdb=" N THR A 236 " --> pdb=" O ARG A 232 " (cutoff:3.500A) Proline residue: A 248 - end of helix removed outlier: 3.624A pdb=" N GLY A 253 " --> pdb=" O TYR A 249 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 300 Proline residue: A 274 - end of helix removed outlier: 3.731A pdb=" N HIS A 283 " --> pdb=" O LEU A 279 " (cutoff:3.500A) removed outlier: 4.644A pdb=" N SER A 284 " --> pdb=" O ALA A 280 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N CYS A 285 " --> pdb=" O LEU A 281 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ASN A 287 " --> pdb=" O HIS A 283 " (cutoff:3.500A) Proline residue: A 288 - end of helix removed outlier: 4.163A pdb=" N TYR A 293 " --> pdb=" O MET A 289 " (cutoff:3.500A) removed outlier: 5.933A pdb=" N ALA A 297 " --> pdb=" O TYR A 293 " (cutoff:3.500A) removed outlier: 6.368A pdb=" N GLN A 298 " --> pdb=" O PHE A 294 " (cutoff:3.500A) Processing helix chain 'A' and resid 301 through 306 removed outlier: 3.795A pdb=" N ALA A 305 " --> pdb=" O ARG A 301 " (cutoff:3.500A) Processing helix chain 'D' and resid 2 through 11 Processing helix chain 'D' and resid 15 through 26 Processing helix chain 'D' and resid 33 through 38 Processing helix chain 'D' and resid 39 through 41 No H-bonds generated for 'chain 'D' and resid 39 through 41' Processing helix chain 'D' and resid 44 through 62 Processing sheet with id=AA1, first strand: chain 'A' and resid 176 through 178 Processing sheet with id=AA2, first strand: chain 'A' and resid 188 through 189 192 hydrogen bonds defined for protein. 561 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.31 Time building geometry restraints manager: 0.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 843 1.35 - 1.48: 656 1.48 - 1.60: 1130 1.60 - 1.72: 0 1.72 - 1.85: 29 Bond restraints: 2658 Sorted by residual: bond pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " ideal model delta sigma weight residual 1.808 1.848 -0.040 3.30e-02 9.18e+02 1.47e+00 bond pdb=" N GLY A 26 " pdb=" CA GLY A 26 " ideal model delta sigma weight residual 1.449 1.464 -0.015 1.45e-02 4.76e+03 1.08e+00 bond pdb=" CB THR A 166 " pdb=" CG2 THR A 166 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.76e-01 bond pdb=" CA ILE D 65 " pdb=" CB ILE D 65 " ideal model delta sigma weight residual 1.545 1.537 0.008 9.10e-03 1.21e+04 7.66e-01 bond pdb=" CA VAL A 167 " pdb=" C VAL A 167 " ideal model delta sigma weight residual 1.524 1.533 -0.008 1.05e-02 9.07e+03 6.26e-01 ... (remaining 2653 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.22: 3465 1.22 - 2.44: 131 2.44 - 3.66: 30 3.66 - 4.88: 16 4.88 - 6.09: 2 Bond angle restraints: 3644 Sorted by residual: angle pdb=" C ALA A 140 " pdb=" N TRP A 141 " pdb=" CA TRP A 141 " ideal model delta sigma weight residual 122.31 117.85 4.46 2.00e+00 2.50e-01 4.97e+00 angle pdb=" N VAL A 167 " pdb=" CA VAL A 167 " pdb=" C VAL A 167 " ideal model delta sigma weight residual 108.88 113.55 -4.67 2.16e+00 2.14e-01 4.67e+00 angle pdb=" CA CYS D 54 " pdb=" CB CYS D 54 " pdb=" SG CYS D 54 " ideal model delta sigma weight residual 114.40 119.26 -4.86 2.30e+00 1.89e-01 4.46e+00 angle pdb=" CG1 ILE A 31 " pdb=" CB ILE A 31 " pdb=" CG2 ILE A 31 " ideal model delta sigma weight residual 110.70 104.61 6.09 3.00e+00 1.11e-01 4.13e+00 angle pdb=" N ASN A 262 " pdb=" CA ASN A 262 " pdb=" CB ASN A 262 " ideal model delta sigma weight residual 113.65 110.74 2.91 1.47e+00 4.63e-01 3.91e+00 ... (remaining 3639 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.23: 1338 11.23 - 22.46: 162 22.46 - 33.68: 48 33.68 - 44.91: 23 44.91 - 56.14: 4 Dihedral angle restraints: 1575 sinusoidal: 539 harmonic: 1036 Sorted by residual: dihedral pdb=" CB CYS D 34 " pdb=" SG CYS D 34 " pdb=" SG CYS D 55 " pdb=" CB CYS D 55 " ideal model delta sinusoidal sigma weight residual -86.00 -131.37 45.37 1 1.00e+01 1.00e-02 2.86e+01 dihedral pdb=" CA ARG A 232 " pdb=" C ARG A 232 " pdb=" N PRO A 233 " pdb=" CA PRO A 233 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 dihedral pdb=" CA HIS A 220 " pdb=" C HIS A 220 " pdb=" N SER A 221 " pdb=" CA SER A 221 " ideal model delta harmonic sigma weight residual 180.00 163.44 16.56 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 1572 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 296 0.035 - 0.071: 106 0.071 - 0.106: 30 0.106 - 0.141: 10 0.141 - 0.177: 2 Chirality restraints: 444 Sorted by residual: chirality pdb=" CB ILE A 31 " pdb=" CA ILE A 31 " pdb=" CG1 ILE A 31 " pdb=" CG2 ILE A 31 " both_signs ideal model delta sigma weight residual False 2.64 2.82 -0.18 2.00e-01 2.50e+01 7.81e-01 chirality pdb=" CA GLU A 273 " pdb=" N GLU A 273 " pdb=" C GLU A 273 " pdb=" CB GLU A 273 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.01e-01 chirality pdb=" CG LEU A 213 " pdb=" CB LEU A 213 " pdb=" CD1 LEU A 213 " pdb=" CD2 LEU A 213 " both_signs ideal model delta sigma weight residual False -2.59 -2.46 -0.13 2.00e-01 2.50e+01 3.97e-01 ... (remaining 441 not shown) Planarity restraints: 458 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ALA A 37 " -0.029 5.00e-02 4.00e+02 4.37e-02 3.06e+00 pdb=" N PRO A 38 " 0.076 5.00e-02 4.00e+02 pdb=" CA PRO A 38 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO A 38 " -0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 211 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.69e+00 pdb=" N PRO A 212 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 212 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 212 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 287 " 0.022 5.00e-02 4.00e+02 3.34e-02 1.79e+00 pdb=" N PRO A 288 " -0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " 0.019 5.00e-02 4.00e+02 ... (remaining 455 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 606 2.79 - 3.32: 2619 3.32 - 3.84: 4287 3.84 - 4.37: 4395 4.37 - 4.90: 7799 Nonbonded interactions: 19706 Sorted by model distance: nonbonded pdb=" NH1 ARG A 173 " pdb=" O CYS A 186 " model vdw 2.260 3.120 nonbonded pdb=" OG SER A 169 " pdb=" NH2 ARG A 204 " model vdw 2.325 3.120 nonbonded pdb=" OD2 ASP A 80 " pdb=" ND2 ASN A 287 " model vdw 2.399 3.120 nonbonded pdb=" OE2 GLU A 178 " pdb=" NE2 GLN A 185 " model vdw 2.403 3.120 nonbonded pdb=" O LEU A 165 " pdb=" NH1 ARG A 204 " model vdw 2.464 3.120 ... (remaining 19701 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 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: 0.050 Check model and map are aligned: 0.000 Set scattering table: 0.010 Process input model: 3.600 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7118 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 2663 Z= 0.163 Angle : 0.639 6.095 3654 Z= 0.334 Chirality : 0.042 0.177 444 Planarity : 0.005 0.044 458 Dihedral : 11.782 51.403 890 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.30 % Favored : 92.70 % Rotamer: Outliers : 0.00 % Allowed : 0.40 % Favored : 99.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.91 (0.47), residues: 356 helix: 1.41 (0.35), residues: 247 sheet: -3.08 (1.38), residues: 10 loop : -0.98 (0.63), residues: 99 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 173 TYR 0.012 0.001 TYR A 119 PHE 0.008 0.001 PHE A 243 TRP 0.009 0.001 TRP A 141 HIS 0.003 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00367 / 0.16 ( 2658) covalent geometry : angle 0.63105 / 0.33 ( 3644) SS BOND : bond 0.00441 / 0.21 ( 5) SS BOND : angle 1.98724 / 1.08 ( 10) hydrogen bonds : bond 0.12554 / 8.80 ( 192) hydrogen bonds : angle 6.02641 / 4.08 ( 561) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 83 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 149 CYS cc_start: 0.6809 (t) cc_final: 0.6596 (t) REVERT: A 252 LEU cc_start: 0.8318 (tp) cc_final: 0.8030 (tt) REVERT: A 271 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7390 (ttm110) outliers start: 0 outliers final: 0 residues processed: 83 average time/residue: 0.0521 time to fit residues: 5.1809 Evaluate side-chains 63 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.106 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 32 optimal weight: 7.9990 chunk 31 optimal weight: 0.0370 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 30 optimal weight: 0.0770 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.8980 overall best weight: 0.4216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 75 HIS A 220 HIS ** A 250 HIS ** 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 = 0.4234 r_free = 0.4234 target = 0.189206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.140670 restraints weight = 3037.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3767 r_free = 0.3767 target = 0.144534 restraints weight = 1892.857| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3793 r_free = 0.3793 target = 0.147095 restraints weight = 1405.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.3806 r_free = 0.3806 target = 0.148457 restraints weight = 1175.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.149799 restraints weight = 1062.683| |-----------------------------------------------------------------------------| r_work (final): 0.3802 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.1903 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 2663 Z= 0.147 Angle : 0.653 8.971 3654 Z= 0.325 Chirality : 0.042 0.139 444 Planarity : 0.006 0.044 458 Dihedral : 4.525 36.232 385 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 3.95 % Allowed : 13.44 % Favored : 82.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.04 (0.47), residues: 356 helix: 1.41 (0.34), residues: 261 sheet: -2.31 (1.46), residues: 10 loop : -1.09 (0.70), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 296 TYR 0.013 0.001 TYR A 190 PHE 0.008 0.001 PHE A 243 TRP 0.009 0.001 TRP A 141 HIS 0.014 0.003 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.15 ( 2658) covalent geometry : angle 0.63952 / 0.32 ( 3644) SS BOND : bond 0.00661 / 0.31 ( 5) SS BOND : angle 2.57737 / 1.45 ( 10) hydrogen bonds : bond 0.04241 / 2.82 ( 192) hydrogen bonds : angle 5.34104 / 3.63 ( 561) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 62 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 55 MET cc_start: 0.8262 (OUTLIER) cc_final: 0.7756 (tpp) REVERT: A 271 ARG cc_start: 0.8129 (mtp85) cc_final: 0.7536 (ttm110) REVERT: A 289 MET cc_start: 0.7716 (mmm) cc_final: 0.7478 (mmt) outliers start: 10 outliers final: 8 residues processed: 65 average time/residue: 0.0581 time to fit residues: 4.5706 Evaluate side-chains 69 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 60 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 55 MET Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 160 THR Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 285 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 7 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 15 optimal weight: 1.9990 chunk 2 optimal weight: 0.0980 chunk 17 optimal weight: 2.9990 chunk 16 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 18 optimal weight: 0.5980 chunk 23 optimal weight: 0.0060 chunk 12 optimal weight: 1.9990 overall best weight: 0.4596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 250 HIS ** A 287 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 29 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 67 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4216 r_free = 0.4216 target = 0.188063 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.138685 restraints weight = 3072.267| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.143012 restraints weight = 1859.315| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.145763 restraints weight = 1346.751| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3789 r_free = 0.3789 target = 0.147234 restraints weight = 1115.423| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.147952 restraints weight = 1000.126| |-----------------------------------------------------------------------------| r_work (final): 0.3806 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7232 moved from start: 0.2272 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2663 Z= 0.138 Angle : 0.626 6.451 3654 Z= 0.313 Chirality : 0.041 0.131 444 Planarity : 0.005 0.040 458 Dihedral : 4.400 37.014 385 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 7.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.34 % Favored : 94.66 % Rotamer: Outliers : 4.74 % Allowed : 16.60 % Favored : 78.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.14 (0.48), residues: 356 helix: 1.58 (0.34), residues: 255 sheet: -2.23 (1.44), residues: 10 loop : -1.23 (0.69), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 147 TYR 0.014 0.001 TYR A 293 PHE 0.008 0.001 PHE D 51 TRP 0.009 0.001 TRP A 141 HIS 0.010 0.002 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00316 / 0.14 ( 2658) covalent geometry : angle 0.61283 / 0.31 ( 3644) SS BOND : bond 0.00639 / 0.29 ( 5) SS BOND : angle 2.51747 / 1.41 ( 10) hydrogen bonds : bond 0.03904 / 2.59 ( 192) hydrogen bonds : angle 5.15054 / 3.52 ( 561) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 63 time to evaluate : 0.087 Fit side-chains REVERT: A 55 MET cc_start: 0.8365 (ttp) cc_final: 0.7864 (tpp) REVERT: A 135 LEU cc_start: 0.7723 (OUTLIER) cc_final: 0.7251 (tt) REVERT: A 252 LEU cc_start: 0.8444 (tp) cc_final: 0.8228 (tt) REVERT: A 271 ARG cc_start: 0.8171 (mtp85) cc_final: 0.7587 (ttm110) outliers start: 12 outliers final: 9 residues processed: 68 average time/residue: 0.0474 time to fit residues: 4.0156 Evaluate side-chains 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 54 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 285 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 26 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 7 optimal weight: 1.9990 chunk 31 optimal weight: 8.9990 chunk 10 optimal weight: 0.5980 chunk 14 optimal weight: 0.7980 chunk 8 optimal weight: 0.0770 chunk 28 optimal weight: 4.9990 chunk 23 optimal weight: 0.6980 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 29 ASN D 67 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.186193 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3677 r_free = 0.3677 target = 0.136857 restraints weight = 3089.415| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.141003 restraints weight = 1896.494| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.143805 restraints weight = 1388.395| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145113 restraints weight = 1146.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 22)----------------| | r_work = 0.3770 r_free = 0.3770 target = 0.145113 restraints weight = 1035.310| |-----------------------------------------------------------------------------| r_work (final): 0.3765 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7265 moved from start: 0.2500 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2663 Z= 0.141 Angle : 0.621 6.397 3654 Z= 0.312 Chirality : 0.041 0.135 444 Planarity : 0.005 0.039 458 Dihedral : 4.328 36.876 385 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.32 % Allowed : 18.18 % Favored : 75.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.12 (0.48), residues: 356 helix: 1.58 (0.35), residues: 254 sheet: -2.12 (1.45), residues: 10 loop : -1.28 (0.69), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.015 0.001 TYR A 293 PHE 0.023 0.002 PHE A 291 TRP 0.009 0.001 TRP A 141 HIS 0.006 0.001 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 2658) covalent geometry : angle 0.60786 / 0.31 ( 3644) SS BOND : bond 0.00588 / 0.27 ( 5) SS BOND : angle 2.49438 / 1.40 ( 10) hydrogen bonds : bond 0.03852 / 2.56 ( 192) hydrogen bonds : angle 5.05809 / 3.47 ( 561) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.111 Fit side-chains REVERT: A 55 MET cc_start: 0.8390 (ttp) cc_final: 0.7889 (tpp) REVERT: A 58 TRP cc_start: 0.8353 (t-100) cc_final: 0.8115 (t-100) REVERT: A 252 LEU cc_start: 0.8463 (tp) cc_final: 0.8243 (tt) REVERT: A 271 ARG cc_start: 0.8186 (mtp85) cc_final: 0.7745 (ttm110) REVERT: D 71 GLN cc_start: 0.6862 (OUTLIER) cc_final: 0.5448 (mp10) outliers start: 16 outliers final: 14 residues processed: 69 average time/residue: 0.0427 time to fit residues: 3.7113 Evaluate side-chains 75 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 60 time to evaluate : 0.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 71 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 5 optimal weight: 1.9990 chunk 32 optimal weight: 4.9990 chunk 11 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 4 optimal weight: 5.9990 chunk 16 optimal weight: 0.2980 chunk 27 optimal weight: 0.3980 chunk 19 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 0.0970 overall best weight: 0.4378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... D 67 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.187976 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3692 r_free = 0.3692 target = 0.138159 restraints weight = 3063.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142305 restraints weight = 1908.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.145032 restraints weight = 1400.444| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146532 restraints weight = 1160.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.147911 restraints weight = 1040.388| |-----------------------------------------------------------------------------| r_work (final): 0.3792 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7207 moved from start: 0.2679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2663 Z= 0.134 Angle : 0.620 6.357 3654 Z= 0.312 Chirality : 0.041 0.129 444 Planarity : 0.005 0.038 458 Dihedral : 4.236 35.800 385 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 5.14 % Allowed : 21.34 % Favored : 73.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.15 (0.48), residues: 356 helix: 1.59 (0.35), residues: 254 sheet: -1.67 (1.48), residues: 10 loop : -1.29 (0.69), residues: 92 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 296 TYR 0.015 0.001 TYR A 293 PHE 0.034 0.002 PHE A 291 TRP 0.008 0.001 TRP A 141 HIS 0.020 0.003 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 ( 2658) covalent geometry : angle 0.60512 / 0.31 ( 3644) SS BOND : bond 0.00597 / 0.28 ( 5) SS BOND : angle 2.68203 / 1.50 ( 10) hydrogen bonds : bond 0.03715 / 2.45 ( 192) hydrogen bonds : angle 4.96013 / 3.40 ( 561) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 0.094 Fit side-chains REVERT: A 55 MET cc_start: 0.8416 (ttp) cc_final: 0.7907 (tpp) REVERT: A 58 TRP cc_start: 0.8365 (t-100) cc_final: 0.8165 (t-100) REVERT: A 252 LEU cc_start: 0.8401 (tp) cc_final: 0.8182 (tt) REVERT: A 271 ARG cc_start: 0.8206 (mtp85) cc_final: 0.7618 (ttm110) REVERT: D 71 GLN cc_start: 0.6833 (OUTLIER) cc_final: 0.5385 (mp10) outliers start: 13 outliers final: 11 residues processed: 69 average time/residue: 0.0493 time to fit residues: 4.2383 Evaluate side-chains 72 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 60 time to evaluate : 0.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain D residue 71 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 1 optimal weight: 0.9980 chunk 9 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 30 optimal weight: 5.9990 chunk 8 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 2 optimal weight: 0.0030 chunk 13 optimal weight: 0.6980 chunk 10 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.5390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS D 29 ASN ** D 67 HIS ** 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 = 0.4220 r_free = 0.4220 target = 0.187267 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137519 restraints weight = 3031.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141590 restraints weight = 1889.996| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3758 r_free = 0.3758 target = 0.143958 restraints weight = 1395.998| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.145998 restraints weight = 1168.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.146867 restraints weight = 1040.849| |-----------------------------------------------------------------------------| r_work (final): 0.3786 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.2811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 2663 Z= 0.143 Angle : 0.638 6.694 3654 Z= 0.320 Chirality : 0.041 0.131 444 Planarity : 0.005 0.038 458 Dihedral : 4.273 36.567 385 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 6.72 % Allowed : 21.74 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.15 (0.48), residues: 356 helix: 1.52 (0.35), residues: 255 sheet: -0.88 (1.59), residues: 10 loop : -1.17 (0.71), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.015 0.001 TYR A 293 PHE 0.033 0.002 PHE A 291 TRP 0.008 0.001 TRP A 141 HIS 0.013 0.002 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00340 / 0.14 ( 2658) covalent geometry : angle 0.62360 / 0.31 ( 3644) SS BOND : bond 0.00602 / 0.28 ( 5) SS BOND : angle 2.63592 / 1.48 ( 10) hydrogen bonds : bond 0.03805 / 2.52 ( 192) hydrogen bonds : angle 5.04309 / 3.48 ( 561) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 58 time to evaluate : 0.108 Fit side-chains REVERT: A 252 LEU cc_start: 0.8432 (tp) cc_final: 0.8211 (tt) REVERT: A 271 ARG cc_start: 0.8198 (mtp85) cc_final: 0.7628 (ttm110) REVERT: A 289 MET cc_start: 0.7513 (tpp) cc_final: 0.6978 (tpp) REVERT: D 71 GLN cc_start: 0.6786 (OUTLIER) cc_final: 0.5304 (mp10) outliers start: 17 outliers final: 15 residues processed: 67 average time/residue: 0.0453 time to fit residues: 3.7881 Evaluate side-chains 74 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 58 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 71 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 4 optimal weight: 5.9990 chunk 27 optimal weight: 0.6980 chunk 17 optimal weight: 0.6980 chunk 29 optimal weight: 7.9990 chunk 3 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 26 optimal weight: 0.5980 chunk 2 optimal weight: 0.5980 chunk 18 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS ** D 67 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4220 r_free = 0.4220 target = 0.186982 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137148 restraints weight = 3155.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.141189 restraints weight = 1954.987| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144006 restraints weight = 1439.815| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3772 r_free = 0.3772 target = 0.145491 restraints weight = 1194.681| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3777 r_free = 0.3777 target = 0.145952 restraints weight = 1071.664| |-----------------------------------------------------------------------------| r_work (final): 0.3783 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 moved from start: 0.2926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 2663 Z= 0.154 Angle : 0.664 6.739 3654 Z= 0.337 Chirality : 0.042 0.198 444 Planarity : 0.005 0.038 458 Dihedral : 4.255 36.782 385 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 7.11 % Allowed : 21.74 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.09 (0.48), residues: 356 helix: 1.47 (0.35), residues: 255 sheet: 0.08 (1.82), residues: 10 loop : -1.30 (0.69), residues: 91 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.015 0.001 TYR A 293 PHE 0.036 0.002 PHE A 291 TRP 0.008 0.001 TRP A 141 HIS 0.007 0.002 HIS A 176 Details of bonding type rmsd/Z covalent geometry : bond 0.00372 / 0.15 ( 2658) covalent geometry : angle 0.65059 / 0.33 ( 3644) SS BOND : bond 0.00595 / 0.28 ( 5) SS BOND : angle 2.65146 / 1.48 ( 10) hydrogen bonds : bond 0.03856 / 2.55 ( 192) hydrogen bonds : angle 5.08700 / 3.53 ( 561) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 53 time to evaluate : 0.090 Fit side-chains REVERT: A 55 MET cc_start: 0.8403 (ttt) cc_final: 0.8181 (tpp) REVERT: A 252 LEU cc_start: 0.8490 (tp) cc_final: 0.8272 (tt) REVERT: A 271 ARG cc_start: 0.8188 (mtp85) cc_final: 0.7625 (ttm110) REVERT: D 71 GLN cc_start: 0.6770 (OUTLIER) cc_final: 0.5269 (mp10) outliers start: 18 outliers final: 15 residues processed: 64 average time/residue: 0.0540 time to fit residues: 4.2470 Evaluate side-chains 69 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 LEU Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 68 VAL Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 ILE Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 262 ASN Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 71 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 0.0270 chunk 14 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 34 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 8 optimal weight: 0.0980 chunk 5 optimal weight: 0.7980 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS D 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4213 r_free = 0.4213 target = 0.187425 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3687 r_free = 0.3687 target = 0.137427 restraints weight = 3108.826| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3734 r_free = 0.3734 target = 0.141736 restraints weight = 1887.330| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3766 r_free = 0.3766 target = 0.144653 restraints weight = 1368.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3782 r_free = 0.3782 target = 0.146210 restraints weight = 1121.107| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3797 r_free = 0.3797 target = 0.147510 restraints weight = 1001.102| |-----------------------------------------------------------------------------| r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7174 moved from start: 0.3180 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 2663 Z= 0.138 Angle : 0.648 7.141 3654 Z= 0.326 Chirality : 0.041 0.186 444 Planarity : 0.005 0.038 458 Dihedral : 4.132 34.507 385 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.14 % Allowed : 23.32 % Favored : 71.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.18 (0.48), residues: 356 helix: 1.56 (0.35), residues: 254 sheet: -1.19 (1.55), residues: 12 loop : -1.13 (0.71), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 271 TYR 0.017 0.001 TYR A 293 PHE 0.020 0.001 PHE A 291 TRP 0.008 0.001 TRP A 141 HIS 0.003 0.001 HIS A 220 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 2658) covalent geometry : angle 0.63168 / 0.32 ( 3644) SS BOND : bond 0.00623 / 0.30 ( 5) SS BOND : angle 2.86613 / 1.61 ( 10) hydrogen bonds : bond 0.03681 / 2.42 ( 192) hydrogen bonds : angle 4.92077 / 3.39 ( 561) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.109 Fit side-chains REVERT: A 55 MET cc_start: 0.8495 (ttt) cc_final: 0.8109 (tpp) REVERT: A 185 GLN cc_start: 0.7896 (mt0) cc_final: 0.7660 (pt0) REVERT: A 252 LEU cc_start: 0.8347 (tp) cc_final: 0.8130 (tt) REVERT: A 271 ARG cc_start: 0.8251 (mtp85) cc_final: 0.7735 (ttm110) REVERT: D 71 GLN cc_start: 0.6659 (OUTLIER) cc_final: 0.5180 (mp10) outliers start: 13 outliers final: 11 residues processed: 61 average time/residue: 0.0528 time to fit residues: 3.9645 Evaluate side-chains 64 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 52 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 71 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 30 optimal weight: 0.4980 chunk 15 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 23 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 32 optimal weight: 0.0010 chunk 8 optimal weight: 0.8980 overall best weight: 0.4186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4210 r_free = 0.4210 target = 0.187260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.137853 restraints weight = 3147.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.141986 restraints weight = 1939.713| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3764 r_free = 0.3764 target = 0.144762 restraints weight = 1417.944| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 51)----------------| | r_work = 0.3784 r_free = 0.3784 target = 0.146532 restraints weight = 1174.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.147212 restraints weight = 1047.881| |-----------------------------------------------------------------------------| r_work (final): 0.3800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 2663 Z= 0.137 Angle : 0.649 7.173 3654 Z= 0.326 Chirality : 0.041 0.206 444 Planarity : 0.005 0.037 458 Dihedral : 4.133 35.323 385 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 5.14 % Allowed : 23.72 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.14 (0.48), residues: 356 helix: 1.52 (0.34), residues: 254 sheet: -1.10 (1.67), residues: 12 loop : -1.16 (0.70), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.017 0.001 TYR A 293 PHE 0.019 0.002 PHE A 291 TRP 0.008 0.001 TRP A 141 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.14 ( 2658) covalent geometry : angle 0.63275 / 0.32 ( 3644) SS BOND : bond 0.00608 / 0.29 ( 5) SS BOND : angle 2.79630 / 1.57 ( 10) hydrogen bonds : bond 0.03662 / 2.41 ( 192) hydrogen bonds : angle 4.89643 / 3.38 ( 561) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 53 time to evaluate : 0.054 Fit side-chains REVERT: A 55 MET cc_start: 0.8312 (ttt) cc_final: 0.7953 (tpp) REVERT: A 185 GLN cc_start: 0.7939 (mt0) cc_final: 0.7654 (pt0) REVERT: A 252 LEU cc_start: 0.8403 (tp) cc_final: 0.8191 (tt) REVERT: A 271 ARG cc_start: 0.8196 (mtp85) cc_final: 0.7738 (ttm110) REVERT: D 71 GLN cc_start: 0.6671 (OUTLIER) cc_final: 0.5197 (mp10) outliers start: 13 outliers final: 12 residues processed: 62 average time/residue: 0.0508 time to fit residues: 3.8475 Evaluate side-chains 65 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 52 time to evaluate : 0.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 71 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 3 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 4 optimal weight: 6.9990 chunk 15 optimal weight: 0.0570 chunk 2 optimal weight: 0.0030 chunk 11 optimal weight: 0.7980 chunk 29 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 25 optimal weight: 0.7980 chunk 0 optimal weight: 8.9990 chunk 5 optimal weight: 0.6980 overall best weight: 0.4108 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS D 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4214 r_free = 0.4214 target = 0.187818 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.137920 restraints weight = 3171.942| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3738 r_free = 0.3738 target = 0.142253 restraints weight = 1908.217| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3771 r_free = 0.3771 target = 0.145222 restraints weight = 1376.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.146844 restraints weight = 1124.036| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 20)----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.147315 restraints weight = 998.547| |-----------------------------------------------------------------------------| r_work (final): 0.3805 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.3384 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 2663 Z= 0.137 Angle : 0.647 7.095 3654 Z= 0.325 Chirality : 0.041 0.175 444 Planarity : 0.004 0.037 458 Dihedral : 4.104 36.079 385 Min Nonbonded Distance : 2.612 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 5.93 % Allowed : 22.92 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 1.08 (0.48), residues: 356 helix: 1.50 (0.34), residues: 253 sheet: -1.50 (1.51), residues: 14 loop : -1.13 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 147 TYR 0.017 0.001 TYR A 293 PHE 0.012 0.001 PHE A 291 TRP 0.009 0.001 TRP A 141 HIS 0.003 0.001 HIS A 250 Details of bonding type rmsd/Z covalent geometry : bond 0.00323 / 0.14 ( 2658) covalent geometry : angle 0.63038 / 0.32 ( 3644) SS BOND : bond 0.00610 / 0.29 ( 5) SS BOND : angle 2.82778 / 1.59 ( 10) hydrogen bonds : bond 0.03628 / 2.39 ( 192) hydrogen bonds : angle 4.86459 / 3.36 ( 561) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 712 Ramachandran restraints generated. 356 Oldfield, 0 Emsley, 356 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.092 Fit side-chains REVERT: A 66 ARG cc_start: 0.7530 (mtt180) cc_final: 0.7284 (ptt180) REVERT: A 185 GLN cc_start: 0.8074 (mt0) cc_final: 0.7762 (pt0) REVERT: A 252 LEU cc_start: 0.8347 (tp) cc_final: 0.8125 (tt) REVERT: A 271 ARG cc_start: 0.8243 (mtp85) cc_final: 0.7756 (ttm110) REVERT: A 289 MET cc_start: 0.7584 (tpp) cc_final: 0.6991 (tpp) REVERT: D 71 GLN cc_start: 0.6536 (OUTLIER) cc_final: 0.5137 (mp10) outliers start: 15 outliers final: 14 residues processed: 64 average time/residue: 0.0571 time to fit residues: 4.4390 Evaluate side-chains 69 residues out of total 279 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 54 time to evaluate : 0.091 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 47 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 112 SER Chi-restraints excluded: chain A residue 132 LEU Chi-restraints excluded: chain A residue 135 LEU Chi-restraints excluded: chain A residue 149 CYS Chi-restraints excluded: chain A residue 210 LEU Chi-restraints excluded: chain A residue 218 SER Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 285 CYS Chi-restraints excluded: chain D residue 1 THR Chi-restraints excluded: chain D residue 29 ASN Chi-restraints excluded: chain D residue 71 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 35 random chunks: chunk 31 optimal weight: 10.0000 chunk 21 optimal weight: 0.7980 chunk 30 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 8 optimal weight: 0.6980 chunk 14 optimal weight: 2.9990 chunk 29 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 23 optimal weight: 0.5980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 220 HIS D 29 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4198 r_free = 0.4198 target = 0.185716 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.136187 restraints weight = 3204.654| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.140206 restraints weight = 1992.148| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.142840 restraints weight = 1463.552| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.3757 r_free = 0.3757 target = 0.144142 restraints weight = 1213.508| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3760 r_free = 0.3760 target = 0.144398 restraints weight = 1094.206| |-----------------------------------------------------------------------------| r_work (final): 0.3748 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7283 moved from start: 0.3388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 2663 Z= 0.163 Angle : 0.676 6.778 3654 Z= 0.341 Chirality : 0.043 0.206 444 Planarity : 0.004 0.033 458 Dihedral : 4.229 38.284 385 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.78 % Favored : 95.22 % Rotamer: Outliers : 7.51 % Allowed : 21.34 % Favored : 71.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.26 % 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: 0.97 (0.47), residues: 356 helix: 1.39 (0.34), residues: 255 sheet: -1.14 (1.72), residues: 12 loop : -1.24 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 204 TYR 0.017 0.001 TYR A 293 PHE 0.015 0.002 PHE D 51 TRP 0.009 0.001 TRP A 141 HIS 0.004 0.001 HIS A 179 Details of bonding type rmsd/Z covalent geometry : bond 0.00396 / 0.16 ( 2658) covalent geometry : angle 0.66019 / 0.33 ( 3644) SS BOND : bond 0.00595 / 0.28 ( 5) SS BOND : angle 2.84105 / 1.59 ( 10) hydrogen bonds : bond 0.03879 / 2.58 ( 192) hydrogen bonds : angle 4.97799 / 3.44 ( 561) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 662.37 seconds wall clock time: 12 minutes 4.40 seconds (724.40 seconds total)