Starting phenix.real_space_refine on Wed Jul 1 21:34:20 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/7rtv_24690/07_2026/7rtv_24690.cif Found real_map, /net/cci-nas-00/data/ceres_data/7rtv_24690/07_2026/7rtv_24690.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.96 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2026/7rtv_24690.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2026/7rtv_24690.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2026/7rtv_24690.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2026/7rtv_24690.map" model { file = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2026/7rtv_24690.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7rtv_24690/07_2026/7rtv_24690.cif" } resolution = 3.96 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= 0.044 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 1846 2.51 5 N 460 2.21 5 O 550 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 2881 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2803 Number of conformers: 1 Conformer: "" Number of residues, atoms: 366, 2803 Classifications: {'peptide': 366} Link IDs: {'PTRANS': 7, 'TRANS': 358} Chain breaks: 1 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 0.85, per 1000 atoms: 0.30 Number of scatterers: 2881 At special positions: 0 Unit cell: (62.863, 52.669, 135.92, 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 550 8.00 N 460 7.00 C 1846 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS A 274 " - pdb=" SG CYS A 382 " distance=2.03 Simple disulfide: pdb=" SG CYS A 300 " - pdb=" SG CYS A 367 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG B 1 " - " ASN A 129 " " NAG C 1 " - " ASN A 352 " Time building additional restraints: 0.38 Conformation dependent library (CDL) restraints added in 138.6 milliseconds 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 680 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 0 sheets defined 92.1% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.04 Creating SS restraints... Processing helix chain 'A' and resid 39 through 73 removed outlier: 4.152A pdb=" N CYS A 73 " --> pdb=" O CYS A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 161 Processing helix chain 'A' and resid 162 through 164 No H-bonds generated for 'chain 'A' and resid 162 through 164' Processing helix chain 'A' and resid 167 through 187 Processing helix chain 'A' and resid 191 through 236 Processing helix chain 'A' and resid 240 through 274 removed outlier: 3.951A pdb=" N LEU A 246 " --> pdb=" O LEU A 242 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N CYS A 247 " --> pdb=" O ALA A 243 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N CYS A 248 " --> pdb=" O SER A 244 " (cutoff:3.500A) Processing helix chain 'A' and resid 276 through 286 removed outlier: 4.318A pdb=" N TYR A 280 " --> pdb=" O ALA A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 290 through 299 removed outlier: 3.530A pdb=" N THR A 294 " --> pdb=" O ASN A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 333 removed outlier: 3.507A pdb=" N LEU A 312 " --> pdb=" O PHE A 308 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 366 removed outlier: 3.618A pdb=" N GLU A 341 " --> pdb=" O PHE A 337 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 366 " --> pdb=" O THR A 362 " (cutoff:3.500A) Processing helix chain 'A' and resid 367 through 409 removed outlier: 4.054A pdb=" N ASP A 384 " --> pdb=" O GLY A 380 " (cutoff:3.500A) removed outlier: 4.508A pdb=" N GLU A 387 " --> pdb=" O TYR A 383 " (cutoff:3.500A) Processing helix chain 'A' and resid 410 through 414 280 hydrogen bonds defined for protein. 834 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: 0.33 Time building geometry restraints manager: 0.48 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: 903 1.34 - 1.46: 530 1.46 - 1.58: 1465 1.58 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 2932 Sorted by residual: bond pdb=" C1 BMA B 3 " pdb=" C2 BMA B 3 " ideal model delta sigma weight residual 1.519 1.574 -0.055 2.00e-02 2.50e+03 7.58e+00 bond pdb=" C1 BMA B 3 " pdb=" O5 BMA B 3 " ideal model delta sigma weight residual 1.410 1.452 -0.042 2.00e-02 2.50e+03 4.32e+00 bond pdb=" C1 NAG B 2 " pdb=" O5 NAG B 2 " ideal model delta sigma weight residual 1.406 1.446 -0.040 2.00e-02 2.50e+03 4.09e+00 bond pdb=" C1 BMA C 3 " pdb=" C2 BMA C 3 " ideal model delta sigma weight residual 1.519 1.549 -0.030 2.00e-02 2.50e+03 2.26e+00 bond pdb=" C1 NAG C 2 " pdb=" O5 NAG C 2 " ideal model delta sigma weight residual 1.406 1.435 -0.029 2.00e-02 2.50e+03 2.14e+00 ... (remaining 2927 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.76: 3857 1.76 - 3.52: 101 3.52 - 5.28: 16 5.28 - 7.05: 10 7.05 - 8.81: 5 Bond angle restraints: 3989 Sorted by residual: angle pdb=" C GLN A 176 " pdb=" N MET A 177 " pdb=" CA MET A 177 " ideal model delta sigma weight residual 121.58 113.37 8.21 1.95e+00 2.63e-01 1.77e+01 angle pdb=" CA MET A 177 " pdb=" CB MET A 177 " pdb=" CG MET A 177 " ideal model delta sigma weight residual 114.10 120.21 -6.11 2.00e+00 2.50e-01 9.33e+00 angle pdb=" CB MET A 174 " pdb=" CG MET A 174 " pdb=" SD MET A 174 " ideal model delta sigma weight residual 112.70 121.51 -8.81 3.00e+00 1.11e-01 8.62e+00 angle pdb=" N MET A 177 " pdb=" CA MET A 177 " pdb=" CB MET A 177 " ideal model delta sigma weight residual 110.41 115.33 -4.92 1.68e+00 3.54e-01 8.59e+00 angle pdb=" CA GLN A 144 " pdb=" CB GLN A 144 " pdb=" CG GLN A 144 " ideal model delta sigma weight residual 114.10 119.15 -5.05 2.00e+00 2.50e-01 6.37e+00 ... (remaining 3984 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.63: 1498 16.63 - 33.27: 140 33.27 - 49.90: 34 49.90 - 66.53: 5 66.53 - 83.17: 5 Dihedral angle restraints: 1682 sinusoidal: 624 harmonic: 1058 Sorted by residual: dihedral pdb=" CB CYS A 274 " pdb=" SG CYS A 274 " pdb=" SG CYS A 382 " pdb=" CB CYS A 382 " ideal model delta sinusoidal sigma weight residual 93.00 172.83 -79.83 1 1.00e+01 1.00e-02 7.90e+01 dihedral pdb=" CB CYS A 300 " pdb=" SG CYS A 300 " pdb=" SG CYS A 367 " pdb=" CB CYS A 367 " ideal model delta sinusoidal sigma weight residual 93.00 132.56 -39.56 1 1.00e+01 1.00e-02 2.20e+01 dihedral pdb=" CA GLN A 331 " pdb=" C GLN A 331 " pdb=" N PHE A 332 " pdb=" CA PHE A 332 " ideal model delta harmonic sigma weight residual 180.00 164.52 15.48 0 5.00e+00 4.00e-02 9.58e+00 ... (remaining 1679 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.054: 412 0.054 - 0.107: 78 0.107 - 0.161: 7 0.161 - 0.214: 3 0.214 - 0.268: 2 Chirality restraints: 502 Sorted by residual: chirality pdb=" C5 BMA C 3 " pdb=" C4 BMA C 3 " pdb=" C6 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" C1 NAG B 1 " pdb=" ND2 ASN A 129 " pdb=" C2 NAG B 1 " pdb=" O5 NAG B 1 " both_signs ideal model delta sigma weight residual False -2.40 -2.20 -0.20 2.00e-01 2.50e+01 9.52e-01 ... (remaining 499 not shown) Planarity restraints: 488 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLY A 410 " -0.053 5.00e-02 4.00e+02 8.01e-02 1.03e+01 pdb=" N PRO A 411 " 0.139 5.00e-02 4.00e+02 pdb=" CA PRO A 411 " -0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 411 " -0.044 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 381 " 0.007 2.00e-02 2.50e+03 1.47e-02 2.17e+00 pdb=" C ILE A 381 " -0.026 2.00e-02 2.50e+03 pdb=" O ILE A 381 " 0.010 2.00e-02 2.50e+03 pdb=" N CYS A 382 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 382 " -0.007 2.00e-02 2.50e+03 1.45e-02 2.11e+00 pdb=" C CYS A 382 " 0.025 2.00e-02 2.50e+03 pdb=" O CYS A 382 " -0.009 2.00e-02 2.50e+03 pdb=" N TYR A 383 " -0.008 2.00e-02 2.50e+03 ... (remaining 485 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 387 2.75 - 3.28: 3201 3.28 - 3.82: 5090 3.82 - 4.36: 5147 4.36 - 4.90: 8800 Nonbonded interactions: 22625 Sorted by model distance: nonbonded pdb=" O SER A 256 " pdb=" OG SER A 396 " model vdw 2.207 3.040 nonbonded pdb=" O GLY A 117 " pdb=" NE2 GLN A 120 " model vdw 2.228 3.120 nonbonded pdb=" O SER A 183 " pdb=" OG SER A 186 " model vdw 2.259 3.040 nonbonded pdb=" O CYS A 300 " pdb=" NH2 ARG A 368 " model vdw 2.308 3.120 nonbonded pdb=" ND2 ASN A 115 " pdb=" OE2 GLU A 209 " model vdw 2.319 3.120 ... (remaining 22620 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 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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: 0.280 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: 0.030 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.480 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:1.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 5.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6306 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 0.055 2940 Z= 0.182 Angle : 0.775 8.808 4011 Z= 0.353 Chirality : 0.045 0.268 502 Planarity : 0.005 0.080 486 Dihedral : 14.212 83.166 996 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 14.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 0.32 % Allowed : 1.95 % Favored : 97.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.61 (0.44), residues: 362 helix: 2.84 (0.28), residues: 321 sheet: None (None), residues: 0 loop : -1.76 (1.14), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 192 TYR 0.015 0.001 TYR A 66 PHE 0.022 0.002 PHE A 220 TRP 0.005 0.001 TRP A 257 HIS 0.003 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00369 / 0.18 ( 2932) covalent geometry : angle 0.76286 / 0.35 ( 3989) SS BOND : bond 0.00287 / 0.15 ( 2) SS BOND : angle 1.91192 / 1.14 ( 4) hydrogen bonds : bond 0.07293 / 3.81 ( 280) hydrogen bonds : angle 4.57725 / 3.46 ( 834) link_BETA1-4 : bond 0.00599 / 0.29 ( 4) link_BETA1-4 : angle 1.29551 / 0.73 ( 12) link_NAG-ASN : bond 0.00600 / 0.31 ( 2) link_NAG-ASN : angle 2.99834 / 1.80 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 93 time to evaluate : 0.104 Fit side-chains REVERT: A 127 ASN cc_start: 0.7972 (m110) cc_final: 0.7152 (m-40) REVERT: A 132 PHE cc_start: 0.7293 (m-80) cc_final: 0.7026 (m-10) REVERT: A 177 MET cc_start: 0.7020 (pmm) cc_final: 0.6598 (pmm) REVERT: A 372 LYS cc_start: 0.8838 (tttp) cc_final: 0.8378 (tttm) outliers start: 1 outliers final: 0 residues processed: 94 average time/residue: 0.0398 time to fit residues: 4.6874 Evaluate side-chains 76 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 24 optimal weight: 0.7980 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 32 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.0270 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 115 ASN ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 152 GLN A 359 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4708 r_free = 0.4708 target = 0.233985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4400 r_free = 0.4400 target = 0.200710 restraints weight = 4378.489| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4460 r_free = 0.4460 target = 0.206761 restraints weight = 2766.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 47)----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.210716 restraints weight = 1942.682| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 26)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.212705 restraints weight = 1483.275| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 39)----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.215135 restraints weight = 1248.626| |-----------------------------------------------------------------------------| r_work (final): 0.4524 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6303 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2940 Z= 0.146 Angle : 0.714 8.091 4011 Z= 0.338 Chirality : 0.043 0.263 502 Planarity : 0.004 0.048 486 Dihedral : 3.984 13.923 389 Min Nonbonded Distance : 2.412 Molprobity Statistics. All-atom Clashscore : 12.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.60 % Allowed : 12.66 % Favored : 84.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.56 (0.43), residues: 362 helix: 2.80 (0.27), residues: 322 sheet: None (None), residues: 0 loop : -1.82 (1.13), residues: 40 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 236 TYR 0.021 0.001 TYR A 296 PHE 0.015 0.002 PHE A 395 TRP 0.004 0.001 TRP A 257 HIS 0.005 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00302 / 0.15 ( 2932) covalent geometry : angle 0.69665 / 0.33 ( 3989) SS BOND : bond 0.00112 / 0.06 ( 2) SS BOND : angle 0.99148 / 0.63 ( 4) hydrogen bonds : bond 0.03584 / 2.27 ( 280) hydrogen bonds : angle 4.15073 / 3.12 ( 834) link_BETA1-4 : bond 0.00915 / 0.45 ( 4) link_BETA1-4 : angle 1.80244 / 1.06 ( 12) link_NAG-ASN : bond 0.00821 / 0.43 ( 2) link_NAG-ASN : angle 3.28805 / 1.97 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.058 Fit side-chains REVERT: A 127 ASN cc_start: 0.7557 (m110) cc_final: 0.6695 (m-40) REVERT: A 177 MET cc_start: 0.7151 (pmm) cc_final: 0.6531 (pmm) REVERT: A 401 LEU cc_start: 0.8769 (OUTLIER) cc_final: 0.8496 (mp) outliers start: 8 outliers final: 4 residues processed: 93 average time/residue: 0.0386 time to fit residues: 4.5296 Evaluate side-chains 84 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 79 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 401 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 1 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 0.0980 chunk 21 optimal weight: 0.9980 chunk 19 optimal weight: 0.6980 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 120 GLN A 152 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4706 r_free = 0.4706 target = 0.233488 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.199188 restraints weight = 4458.938| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4446 r_free = 0.4446 target = 0.205166 restraints weight = 2839.003| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4481 r_free = 0.4481 target = 0.209121 restraints weight = 2006.356| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.211835 restraints weight = 1546.136| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 16)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.213163 restraints weight = 1272.821| |-----------------------------------------------------------------------------| r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6337 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 2940 Z= 0.141 Angle : 0.718 9.845 4011 Z= 0.334 Chirality : 0.041 0.213 502 Planarity : 0.004 0.036 486 Dihedral : 3.994 14.299 389 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 12.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 3.57 % Allowed : 15.91 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.36 (0.43), residues: 362 helix: 2.70 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -2.05 (1.09), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 368 TYR 0.006 0.001 TYR A 66 PHE 0.016 0.002 PHE A 315 TRP 0.007 0.001 TRP A 191 HIS 0.003 0.001 HIS A 359 Details of bonding type rmsd/Z covalent geometry : bond 0.00292 / 0.14 ( 2932) covalent geometry : angle 0.70050 / 0.33 ( 3989) SS BOND : bond 0.00029 / 0.01 ( 2) SS BOND : angle 0.94896 / 0.74 ( 4) hydrogen bonds : bond 0.03448 / 2.22 ( 280) hydrogen bonds : angle 4.11829 / 3.10 ( 834) link_BETA1-4 : bond 0.00817 / 0.40 ( 4) link_BETA1-4 : angle 1.78997 / 1.04 ( 12) link_NAG-ASN : bond 0.00827 / 0.44 ( 2) link_NAG-ASN : angle 3.36533 / 2.02 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.088 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7623 (m110) cc_final: 0.7095 (m-40) REVERT: A 177 MET cc_start: 0.7118 (OUTLIER) cc_final: 0.6657 (pmm) REVERT: A 375 LEU cc_start: 0.8150 (tp) cc_final: 0.7916 (tp) REVERT: A 392 LEU cc_start: 0.7993 (OUTLIER) cc_final: 0.7727 (tt) REVERT: A 401 LEU cc_start: 0.8759 (OUTLIER) cc_final: 0.8441 (mp) outliers start: 11 outliers final: 5 residues processed: 90 average time/residue: 0.0394 time to fit residues: 4.4764 Evaluate side-chains 89 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Chi-restraints excluded: chain A residue 401 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 33 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 24 optimal weight: 0.9990 chunk 20 optimal weight: 5.9990 chunk 2 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 15 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN ** A 120 GLN ** 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 = 0.4703 r_free = 0.4703 target = 0.232110 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4387 r_free = 0.4387 target = 0.197744 restraints weight = 4554.546| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4445 r_free = 0.4445 target = 0.203712 restraints weight = 2924.333| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4483 r_free = 0.4483 target = 0.207765 restraints weight = 2077.150| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.210090 restraints weight = 1610.870| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.212026 restraints weight = 1346.952| |-----------------------------------------------------------------------------| r_work (final): 0.4517 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6348 moved from start: 0.1859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 2940 Z= 0.145 Angle : 0.763 10.472 4011 Z= 0.346 Chirality : 0.045 0.333 502 Planarity : 0.004 0.029 486 Dihedral : 4.036 13.847 389 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 4.87 % Allowed : 17.86 % Favored : 77.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.32 (0.43), residues: 362 helix: 2.66 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.93 (1.13), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 368 TYR 0.005 0.001 TYR A 66 PHE 0.014 0.002 PHE A 395 TRP 0.006 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.14 ( 2932) covalent geometry : angle 0.74579 / 0.34 ( 3989) SS BOND : bond 0.00113 / 0.06 ( 2) SS BOND : angle 1.09736 / 0.90 ( 4) hydrogen bonds : bond 0.03423 / 2.22 ( 280) hydrogen bonds : angle 4.10817 / 3.09 ( 834) link_BETA1-4 : bond 0.00801 / 0.40 ( 4) link_BETA1-4 : angle 1.77731 / 1.04 ( 12) link_NAG-ASN : bond 0.00792 / 0.42 ( 2) link_NAG-ASN : angle 3.49210 / 2.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.057 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7904 (m110) cc_final: 0.7356 (m-40) REVERT: A 143 THR cc_start: 0.8916 (p) cc_final: 0.8490 (t) REVERT: A 177 MET cc_start: 0.7145 (OUTLIER) cc_final: 0.6704 (pmm) REVERT: A 315 PHE cc_start: 0.8310 (OUTLIER) cc_final: 0.8089 (t80) REVERT: A 370 LEU cc_start: 0.7099 (tp) cc_final: 0.6790 (mt) outliers start: 15 outliers final: 10 residues processed: 99 average time/residue: 0.0285 time to fit residues: 3.5959 Evaluate side-chains 95 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 83 time to evaluate : 0.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 19 optimal weight: 3.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 chunk 6 optimal weight: 2.9990 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 0 optimal weight: 1.9990 chunk 14 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 371 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4691 r_free = 0.4691 target = 0.231553 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.197438 restraints weight = 4495.320| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.203492 restraints weight = 2896.903| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.4470 r_free = 0.4470 target = 0.207461 restraints weight = 2054.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4491 r_free = 0.4491 target = 0.209748 restraints weight = 1587.613| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4510 r_free = 0.4510 target = 0.211774 restraints weight = 1328.711| |-----------------------------------------------------------------------------| r_work (final): 0.4506 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6347 moved from start: 0.2126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 2940 Z= 0.142 Angle : 0.758 10.523 4011 Z= 0.353 Chirality : 0.044 0.285 502 Planarity : 0.004 0.053 486 Dihedral : 4.087 14.392 389 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.19 % Allowed : 21.10 % Favored : 73.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.37 (0.44), residues: 362 helix: 2.69 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.84 (1.16), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 192 TYR 0.006 0.001 TYR A 216 PHE 0.013 0.001 PHE A 308 TRP 0.006 0.001 TRP A 213 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 2932) covalent geometry : angle 0.74127 / 0.35 ( 3989) SS BOND : bond 0.00069 / 0.04 ( 2) SS BOND : angle 1.08483 / 0.86 ( 4) hydrogen bonds : bond 0.03429 / 2.21 ( 280) hydrogen bonds : angle 4.11672 / 3.10 ( 834) link_BETA1-4 : bond 0.00783 / 0.39 ( 4) link_BETA1-4 : angle 1.68484 / 1.01 ( 12) link_NAG-ASN : bond 0.00774 / 0.41 ( 2) link_NAG-ASN : angle 3.54197 / 2.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 90 time to evaluate : 0.099 Fit side-chains REVERT: A 127 ASN cc_start: 0.7688 (m110) cc_final: 0.7140 (m-40) REVERT: A 143 THR cc_start: 0.8935 (p) cc_final: 0.8509 (t) REVERT: A 177 MET cc_start: 0.7157 (OUTLIER) cc_final: 0.6701 (pmm) REVERT: A 236 ARG cc_start: 0.5488 (tpp80) cc_final: 0.5041 (tpp-160) REVERT: A 315 PHE cc_start: 0.8418 (OUTLIER) cc_final: 0.8136 (t80) outliers start: 16 outliers final: 11 residues processed: 95 average time/residue: 0.0360 time to fit residues: 4.2541 Evaluate side-chains 96 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 83 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 27 optimal weight: 0.7980 chunk 12 optimal weight: 0.6980 chunk 5 optimal weight: 0.7980 chunk 22 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 25 optimal weight: 0.3980 chunk 26 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 31 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 59 ASN ** A 120 GLN ** 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 = 0.4698 r_free = 0.4698 target = 0.232550 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.198450 restraints weight = 4564.794| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4443 r_free = 0.4443 target = 0.204629 restraints weight = 2896.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.208741 restraints weight = 2044.078| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.4503 r_free = 0.4503 target = 0.211207 restraints weight = 1567.399| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.213158 restraints weight = 1301.201| |-----------------------------------------------------------------------------| r_work (final): 0.4513 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6331 moved from start: 0.2247 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2940 Z= 0.136 Angle : 0.793 11.863 4011 Z= 0.360 Chirality : 0.047 0.378 502 Planarity : 0.005 0.067 486 Dihedral : 4.067 13.528 389 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 13.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 6.17 % Allowed : 22.73 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.41 (0.44), residues: 362 helix: 2.71 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.82 (1.16), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 192 TYR 0.007 0.001 TYR A 41 PHE 0.011 0.001 PHE A 308 TRP 0.006 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00279 / 0.14 ( 2932) covalent geometry : angle 0.77722 / 0.36 ( 3989) SS BOND : bond 0.00054 / 0.03 ( 2) SS BOND : angle 1.05281 / 0.85 ( 4) hydrogen bonds : bond 0.03395 / 2.19 ( 280) hydrogen bonds : angle 4.11762 / 3.10 ( 834) link_BETA1-4 : bond 0.00753 / 0.37 ( 4) link_BETA1-4 : angle 1.71267 / 1.02 ( 12) link_NAG-ASN : bond 0.00797 / 0.42 ( 2) link_NAG-ASN : angle 3.51709 / 2.11 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 86 time to evaluate : 0.091 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7423 (m110) cc_final: 0.6616 (m-40) REVERT: A 143 THR cc_start: 0.8912 (p) cc_final: 0.8506 (t) REVERT: A 177 MET cc_start: 0.6667 (OUTLIER) cc_final: 0.6211 (pmm) REVERT: A 236 ARG cc_start: 0.5484 (tpp80) cc_final: 0.5150 (tpp-160) REVERT: A 315 PHE cc_start: 0.8476 (OUTLIER) cc_final: 0.7928 (t80) REVERT: A 375 LEU cc_start: 0.8517 (tp) cc_final: 0.8291 (tp) outliers start: 19 outliers final: 15 residues processed: 92 average time/residue: 0.0433 time to fit residues: 5.0605 Evaluate side-chains 100 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.090 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 59 ASN Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 7 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 4 optimal weight: 2.9990 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 33 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 9 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 14 optimal weight: 3.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 111 ASN ** A 120 GLN ** 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 = 0.4690 r_free = 0.4690 target = 0.231731 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.198176 restraints weight = 4522.471| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.204260 restraints weight = 2905.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.208183 restraints weight = 2068.454| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4496 r_free = 0.4496 target = 0.210379 restraints weight = 1601.101| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 45)----------------| | r_work = 0.4515 r_free = 0.4515 target = 0.212385 restraints weight = 1341.258| |-----------------------------------------------------------------------------| r_work (final): 0.4511 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2335 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2940 Z= 0.144 Angle : 0.802 11.794 4011 Z= 0.366 Chirality : 0.044 0.301 502 Planarity : 0.005 0.072 486 Dihedral : 4.054 13.382 389 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 15.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 4.87 % Allowed : 24.68 % Favored : 70.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.40 (0.44), residues: 362 helix: 2.70 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.81 (1.16), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 192 TYR 0.009 0.001 TYR A 41 PHE 0.013 0.002 PHE A 308 TRP 0.005 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00298 / 0.14 ( 2932) covalent geometry : angle 0.78657 / 0.36 ( 3989) SS BOND : bond 0.00130 / 0.07 ( 2) SS BOND : angle 1.01526 / 0.77 ( 4) hydrogen bonds : bond 0.03454 / 2.21 ( 280) hydrogen bonds : angle 4.14617 / 3.12 ( 834) link_BETA1-4 : bond 0.00729 / 0.36 ( 4) link_BETA1-4 : angle 1.70256 / 1.01 ( 12) link_NAG-ASN : bond 0.00781 / 0.41 ( 2) link_NAG-ASN : angle 3.53532 / 2.12 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 90 time to evaluate : 0.136 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7421 (m110) cc_final: 0.6654 (m-40) REVERT: A 143 THR cc_start: 0.8914 (p) cc_final: 0.8526 (t) REVERT: A 177 MET cc_start: 0.6682 (OUTLIER) cc_final: 0.6199 (pmm) REVERT: A 236 ARG cc_start: 0.5465 (tpp80) cc_final: 0.5138 (tpp-160) REVERT: A 315 PHE cc_start: 0.8520 (OUTLIER) cc_final: 0.7773 (t80) REVERT: A 375 LEU cc_start: 0.8524 (tp) cc_final: 0.8292 (tp) outliers start: 15 outliers final: 13 residues processed: 95 average time/residue: 0.0561 time to fit residues: 6.6661 Evaluate side-chains 101 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 86 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 34 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 1 optimal weight: 0.8980 chunk 17 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 22 optimal weight: 1.9990 chunk 8 optimal weight: 3.9990 chunk 3 optimal weight: 0.4980 chunk 13 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 11 optimal weight: 3.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4697 r_free = 0.4697 target = 0.232313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.197897 restraints weight = 4711.443| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.204039 restraints weight = 3006.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4474 r_free = 0.4474 target = 0.208275 restraints weight = 2138.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.210658 restraints weight = 1640.728| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 21)----------------| | r_work = 0.4512 r_free = 0.4512 target = 0.212471 restraints weight = 1366.926| |-----------------------------------------------------------------------------| r_work (final): 0.4492 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6368 moved from start: 0.2470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 2940 Z= 0.145 Angle : 0.826 12.632 4011 Z= 0.375 Chirality : 0.046 0.377 502 Planarity : 0.004 0.030 486 Dihedral : 4.068 13.503 389 Min Nonbonded Distance : 2.422 Molprobity Statistics. All-atom Clashscore : 15.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.52 % Allowed : 25.00 % Favored : 69.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.36 (0.44), residues: 362 helix: 2.67 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.79 (1.16), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 368 TYR 0.007 0.001 TYR A 280 PHE 0.012 0.002 PHE A 308 TRP 0.005 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00309 / 0.14 ( 2932) covalent geometry : angle 0.81078 / 0.37 ( 3989) SS BOND : bond 0.00100 / 0.05 ( 2) SS BOND : angle 1.04906 / 0.85 ( 4) hydrogen bonds : bond 0.03441 / 2.23 ( 280) hydrogen bonds : angle 4.21580 / 3.17 ( 834) link_BETA1-4 : bond 0.00744 / 0.37 ( 4) link_BETA1-4 : angle 1.68521 / 1.01 ( 12) link_NAG-ASN : bond 0.00787 / 0.41 ( 2) link_NAG-ASN : angle 3.54438 / 2.13 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.061 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 132 PHE cc_start: 0.7468 (m-80) cc_final: 0.7208 (t80) REVERT: A 143 THR cc_start: 0.8985 (p) cc_final: 0.8628 (t) REVERT: A 177 MET cc_start: 0.6632 (OUTLIER) cc_final: 0.6121 (pmm) REVERT: A 236 ARG cc_start: 0.5629 (tpp80) cc_final: 0.5376 (tpp-160) REVERT: A 315 PHE cc_start: 0.8488 (OUTLIER) cc_final: 0.7219 (t80) REVERT: A 375 LEU cc_start: 0.8523 (tp) cc_final: 0.8289 (tp) outliers start: 17 outliers final: 14 residues processed: 94 average time/residue: 0.0331 time to fit residues: 3.9216 Evaluate side-chains 99 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 9 optimal weight: 0.4980 chunk 23 optimal weight: 0.9990 chunk 33 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 3 optimal weight: 1.9990 chunk 17 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 28 optimal weight: 0.0980 chunk 29 optimal weight: 0.9980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4710 r_free = 0.4710 target = 0.233684 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.199425 restraints weight = 4642.283| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.205535 restraints weight = 2991.111| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4490 r_free = 0.4490 target = 0.209514 restraints weight = 2131.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.211898 restraints weight = 1650.637| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4529 r_free = 0.4529 target = 0.213873 restraints weight = 1376.811| |-----------------------------------------------------------------------------| r_work (final): 0.4522 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6333 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 2940 Z= 0.141 Angle : 0.846 13.075 4011 Z= 0.383 Chirality : 0.044 0.296 502 Planarity : 0.005 0.081 486 Dihedral : 4.127 14.932 389 Min Nonbonded Distance : 2.425 Molprobity Statistics. All-atom Clashscore : 14.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.49 % Favored : 97.51 % Rotamer: Outliers : 5.52 % Allowed : 25.97 % Favored : 68.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.33 (0.44), residues: 362 helix: 2.64 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.69 (1.16), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.017 0.001 ARG A 192 TYR 0.005 0.001 TYR A 109 PHE 0.030 0.002 PHE A 220 TRP 0.005 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.14 ( 2932) covalent geometry : angle 0.83214 / 0.38 ( 3989) SS BOND : bond 0.00091 / 0.04 ( 2) SS BOND : angle 0.92562 / 0.71 ( 4) hydrogen bonds : bond 0.03484 / 2.25 ( 280) hydrogen bonds : angle 4.20480 / 3.17 ( 834) link_BETA1-4 : bond 0.00728 / 0.36 ( 4) link_BETA1-4 : angle 1.70205 / 1.02 ( 12) link_NAG-ASN : bond 0.00799 / 0.42 ( 2) link_NAG-ASN : angle 3.50054 / 2.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 87 time to evaluate : 0.101 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7185 (m110) cc_final: 0.6862 (m-40) REVERT: A 143 THR cc_start: 0.8945 (p) cc_final: 0.8578 (t) REVERT: A 177 MET cc_start: 0.6621 (OUTLIER) cc_final: 0.6145 (pmm) REVERT: A 196 THR cc_start: 0.8468 (OUTLIER) cc_final: 0.8137 (p) REVERT: A 236 ARG cc_start: 0.5533 (tpp80) cc_final: 0.5226 (tpp-160) REVERT: A 315 PHE cc_start: 0.8472 (OUTLIER) cc_final: 0.7169 (t80) REVERT: A 375 LEU cc_start: 0.8480 (tp) cc_final: 0.8271 (tp) outliers start: 17 outliers final: 14 residues processed: 93 average time/residue: 0.0455 time to fit residues: 5.3260 Evaluate side-chains 100 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 83 time to evaluate : 0.085 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 196 THR Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 31 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 chunk 30 optimal weight: 0.8980 chunk 8 optimal weight: 2.9990 chunk 27 optimal weight: 0.5980 chunk 26 optimal weight: 0.0870 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 127 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4707 r_free = 0.4707 target = 0.233431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.196965 restraints weight = 4601.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4440 r_free = 0.4440 target = 0.204102 restraints weight = 2811.777| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4482 r_free = 0.4482 target = 0.208724 restraints weight = 1931.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4511 r_free = 0.4511 target = 0.211776 restraints weight = 1464.643| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4526 r_free = 0.4526 target = 0.213482 restraints weight = 1184.556| |-----------------------------------------------------------------------------| r_work (final): 0.4519 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6340 moved from start: 0.2716 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2940 Z= 0.141 Angle : 0.858 13.824 4011 Z= 0.389 Chirality : 0.044 0.291 502 Planarity : 0.003 0.029 486 Dihedral : 4.052 13.732 389 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 14.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 5.52 % Allowed : 26.30 % Favored : 68.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.27 (0.44), residues: 362 helix: 2.60 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.70 (1.16), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 192 TYR 0.014 0.001 TYR A 296 PHE 0.024 0.002 PHE A 220 TRP 0.007 0.001 TRP A 191 HIS 0.002 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.14 ( 2932) covalent geometry : angle 0.84361 / 0.39 ( 3989) SS BOND : bond 0.00039 / 0.02 ( 2) SS BOND : angle 0.85799 / 0.63 ( 4) hydrogen bonds : bond 0.03440 / 2.22 ( 280) hydrogen bonds : angle 4.31270 / 3.27 ( 834) link_BETA1-4 : bond 0.00719 / 0.36 ( 4) link_BETA1-4 : angle 1.70950 / 1.02 ( 12) link_NAG-ASN : bond 0.00780 / 0.41 ( 2) link_NAG-ASN : angle 3.47473 / 2.08 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 724 Ramachandran restraints generated. 362 Oldfield, 0 Emsley, 362 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 84 time to evaluate : 0.061 Fit side-chains revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7350 (m-40) cc_final: 0.6875 (m-40) REVERT: A 132 PHE cc_start: 0.7138 (m-80) cc_final: 0.6889 (t80) REVERT: A 143 THR cc_start: 0.8915 (p) cc_final: 0.8541 (t) REVERT: A 177 MET cc_start: 0.6610 (OUTLIER) cc_final: 0.6116 (pmm) REVERT: A 236 ARG cc_start: 0.5566 (tpp80) cc_final: 0.5237 (tpp-160) REVERT: A 309 GLN cc_start: 0.7690 (pp30) cc_final: 0.7268 (pp30) REVERT: A 315 PHE cc_start: 0.8349 (OUTLIER) cc_final: 0.7357 (t80) outliers start: 17 outliers final: 14 residues processed: 92 average time/residue: 0.0390 time to fit residues: 4.5644 Evaluate side-chains 99 residues out of total 308 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 83 time to evaluate : 0.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 51 LEU Chi-restraints excluded: chain A residue 122 ILE Chi-restraints excluded: chain A residue 125 LEU Chi-restraints excluded: chain A residue 149 ASP Chi-restraints excluded: chain A residue 177 MET Chi-restraints excluded: chain A residue 226 ILE Chi-restraints excluded: chain A residue 253 LEU Chi-restraints excluded: chain A residue 259 SER Chi-restraints excluded: chain A residue 274 CYS Chi-restraints excluded: chain A residue 294 THR Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 315 PHE Chi-restraints excluded: chain A residue 350 LEU Chi-restraints excluded: chain A residue 365 LEU Chi-restraints excluded: chain A residue 389 LEU Chi-restraints excluded: chain A residue 392 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 36 random chunks: chunk 12 optimal weight: 0.5980 chunk 25 optimal weight: 8.9990 chunk 11 optimal weight: 5.9990 chunk 9 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 33 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 30 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** A 59 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4694 r_free = 0.4694 target = 0.231950 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.196348 restraints weight = 4538.181| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4433 r_free = 0.4433 target = 0.203307 restraints weight = 2789.377| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4476 r_free = 0.4476 target = 0.207787 restraints weight = 1925.237| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.209958 restraints weight = 1457.843| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.4517 r_free = 0.4517 target = 0.212379 restraints weight = 1219.827| |-----------------------------------------------------------------------------| r_work (final): 0.4507 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6355 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 2940 Z= 0.149 Angle : 0.857 13.527 4011 Z= 0.394 Chirality : 0.045 0.284 502 Planarity : 0.004 0.048 486 Dihedral : 4.116 14.585 389 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 5.19 % Allowed : 28.25 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: 3.26 (0.43), residues: 362 helix: 2.58 (0.27), residues: 321 sheet: None (None), residues: 0 loop : -1.58 (1.14), residues: 41 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 192 TYR 0.013 0.001 TYR A 296 PHE 0.024 0.002 PHE A 220 TRP 0.007 0.001 TRP A 191 HIS 0.003 0.001 HIS A 153 Details of bonding type rmsd/Z covalent geometry : bond 0.00315 / 0.15 ( 2932) covalent geometry : angle 0.84323 / 0.39 ( 3989) SS BOND : bond 0.00085 / 0.04 ( 2) SS BOND : angle 0.98343 / 0.70 ( 4) hydrogen bonds : bond 0.03448 / 2.22 ( 280) hydrogen bonds : angle 4.29426 / 3.25 ( 834) link_BETA1-4 : bond 0.00781 / 0.39 ( 4) link_BETA1-4 : angle 1.73015 / 1.03 ( 12) link_NAG-ASN : bond 0.00773 / 0.41 ( 2) link_NAG-ASN : angle 3.47192 / 2.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 588.42 seconds wall clock time: 10 minutes 51.47 seconds (651.47 seconds total)