Starting phenix.real_space_refine on Tue Jan 13 10:54:49 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7uui_26799/01_2026/7uui_26799.cif Found real_map, /net/cci-nas-00/data/ceres_data/7uui_26799/01_2026/7uui_26799.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7uui_26799/01_2026/7uui_26799.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7uui_26799/01_2026/7uui_26799.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7uui_26799/01_2026/7uui_26799.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7uui_26799/01_2026/7uui_26799.map" } resolution = 2.9 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= 0.010 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: 7 Type Number sf(0) Gaussians K 1 8.98 5 P 2 5.49 5 Mg 1 5.21 5 S 10 5.16 5 C 2318 2.51 5 N 666 2.21 5 O 674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5927/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3672 Number of models: 1 Model: "" Number of chains: 2 Chain: "m" Number of atoms: 3642 Number of conformers: 1 Conformer: "" Number of residues, atoms: 452, 3642 Classifications: {'peptide': 452} Link IDs: {'PTRANS': 22, 'TRANS': 429} Chain breaks: 2 Chain: "m" Number of atoms: 30 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 30 Unusual residues: {' K': 1, ' MG': 1, 'GDP': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Time building chain proxies: 1.06, per 1000 atoms: 0.29 Number of scatterers: 3672 At special positions: 0 Unit cell: (113.4, 90.72, 99.36, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) K 1 19.00 S 10 16.00 P 2 15.00 Mg 1 11.99 O 674 8.00 N 666 7.00 C 2318 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 0.33 Conformation dependent library (CDL) restraints added in 156.4 milliseconds 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 848 Finding SS restraints... Secondary structure from input PDB file: 26 helices and 1 sheets defined 54.4% alpha, 6.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.10 Creating SS restraints... Processing helix chain 'm' and resid 2 through 5 Processing helix chain 'm' and resid 6 through 14 Processing helix chain 'm' and resid 32 through 40 Processing helix chain 'm' and resid 41 through 44 Processing helix chain 'm' and resid 74 through 79 removed outlier: 3.645A pdb=" N PHE m 78 " --> pdb=" O ARG m 75 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N GLY m 79 " --> pdb=" O ARG m 76 " (cutoff:3.500A) Processing helix chain 'm' and resid 85 through 102 removed outlier: 3.836A pdb=" N LYS m 101 " --> pdb=" O GLY m 97 " (cutoff:3.500A) removed outlier: 4.256A pdb=" N ASP m 102 " --> pdb=" O GLU m 98 " (cutoff:3.500A) Processing helix chain 'm' and resid 109 through 113 Processing helix chain 'm' and resid 114 through 118 Processing helix chain 'm' and resid 130 through 135 removed outlier: 4.619A pdb=" N THR m 134 " --> pdb=" O ARG m 130 " (cutoff:3.500A) Processing helix chain 'm' and resid 136 through 141 Processing helix chain 'm' and resid 156 through 180 removed outlier: 3.755A pdb=" N THR m 180 " --> pdb=" O VAL m 176 " (cutoff:3.500A) Processing helix chain 'm' and resid 185 through 192 Processing helix chain 'm' and resid 200 through 205 Processing helix chain 'm' and resid 208 through 222 Processing helix chain 'm' and resid 233 through 238 Processing helix chain 'm' and resid 239 through 250 Processing helix chain 'm' and resid 266 through 278 Processing helix chain 'm' and resid 295 through 310 Processing helix chain 'm' and resid 327 through 337 Processing helix chain 'm' and resid 378 through 385 Processing helix chain 'm' and resid 389 through 393 Processing helix chain 'm' and resid 396 through 398 No H-bonds generated for 'chain 'm' and resid 396 through 398' Processing helix chain 'm' and resid 399 through 405 removed outlier: 3.750A pdb=" N VAL m 403 " --> pdb=" O TYR m 399 " (cutoff:3.500A) Processing helix chain 'm' and resid 408 through 417 Processing helix chain 'm' and resid 423 through 436 Processing helix chain 'm' and resid 445 through 459 Processing sheet with id=AA1, first strand: chain 'm' and resid 283 through 285 164 hydrogen bonds defined for protein. 450 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: 0.56 Time building geometry restraints manager: 0.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1200 1.34 - 1.45: 435 1.45 - 1.57: 2092 1.57 - 1.69: 3 1.69 - 1.81: 15 Bond restraints: 3745 Sorted by residual: bond pdb=" C5 GDP m 503 " pdb=" C4 GDP m 503 " ideal model delta sigma weight residual 1.490 1.468 0.022 2.00e-02 2.50e+03 1.24e+00 bond pdb=" C GLN m 354 " pdb=" O GLN m 354 " ideal model delta sigma weight residual 1.234 1.223 0.012 1.11e-02 8.12e+03 1.11e+00 bond pdb=" CA GLN m 308 " pdb=" CB GLN m 308 " ideal model delta sigma weight residual 1.528 1.542 -0.014 1.66e-02 3.63e+03 6.69e-01 bond pdb=" CA ASN m 292 " pdb=" C ASN m 292 " ideal model delta sigma weight residual 1.522 1.530 -0.007 1.18e-02 7.18e+03 3.68e-01 bond pdb=" N GLN m 308 " pdb=" CA GLN m 308 " ideal model delta sigma weight residual 1.459 1.466 -0.008 1.28e-02 6.10e+03 3.49e-01 ... (remaining 3740 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.18: 4906 1.18 - 2.36: 104 2.36 - 3.55: 28 3.55 - 4.73: 7 4.73 - 5.91: 4 Bond angle restraints: 5049 Sorted by residual: angle pdb=" N GLN m 308 " pdb=" CA GLN m 308 " pdb=" CB GLN m 308 " ideal model delta sigma weight residual 110.28 115.23 -4.95 1.55e+00 4.16e-01 1.02e+01 angle pdb=" CA GLN m 308 " pdb=" CB GLN m 308 " pdb=" CG GLN m 308 " ideal model delta sigma weight residual 114.10 118.47 -4.37 2.00e+00 2.50e-01 4.78e+00 angle pdb=" C SER m 307 " pdb=" N GLN m 308 " pdb=" CA GLN m 308 " ideal model delta sigma weight residual 120.31 117.00 3.31 1.52e+00 4.33e-01 4.75e+00 angle pdb=" C3' GDP m 503 " pdb=" C2' GDP m 503 " pdb=" C1' GDP m 503 " ideal model delta sigma weight residual 111.00 105.09 5.91 3.00e+00 1.11e-01 3.88e+00 angle pdb=" C4' GDP m 503 " pdb=" C3' GDP m 503 " pdb=" C2' GDP m 503 " ideal model delta sigma weight residual 111.00 105.86 5.14 3.00e+00 1.11e-01 2.94e+00 ... (remaining 5044 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.37: 2053 17.37 - 34.73: 198 34.73 - 52.10: 27 52.10 - 69.47: 12 69.47 - 86.83: 6 Dihedral angle restraints: 2296 sinusoidal: 987 harmonic: 1309 Sorted by residual: dihedral pdb=" C5' GDP m 503 " pdb=" O5' GDP m 503 " pdb=" PA GDP m 503 " pdb=" O3A GDP m 503 " ideal model delta sinusoidal sigma weight residual 179.98 -108.26 -71.76 1 2.00e+01 2.50e-03 1.65e+01 dihedral pdb=" CB GLU m 244 " pdb=" CG GLU m 244 " pdb=" CD GLU m 244 " pdb=" OE1 GLU m 244 " ideal model delta sinusoidal sigma weight residual 0.00 86.83 -86.83 1 3.00e+01 1.11e-03 1.01e+01 dihedral pdb=" CB GLU m 349 " pdb=" CG GLU m 349 " pdb=" CD GLU m 349 " pdb=" OE1 GLU m 349 " ideal model delta sinusoidal sigma weight residual 0.00 85.20 -85.20 1 3.00e+01 1.11e-03 9.77e+00 ... (remaining 2293 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 326 0.029 - 0.057: 140 0.057 - 0.086: 57 0.086 - 0.114: 22 0.114 - 0.143: 5 Chirality restraints: 550 Sorted by residual: chirality pdb=" CA ILE m 462 " pdb=" N ILE m 462 " pdb=" C ILE m 462 " pdb=" CB ILE m 462 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.14 2.00e-01 2.50e+01 5.09e-01 chirality pdb=" CA ILE m 356 " pdb=" N ILE m 356 " pdb=" C ILE m 356 " pdb=" CB ILE m 356 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 chirality pdb=" CA VAL m 224 " pdb=" N VAL m 224 " pdb=" C VAL m 224 " pdb=" CB VAL m 224 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.05e-01 ... (remaining 547 not shown) Planarity restraints: 641 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C CYS m 367 " -0.021 5.00e-02 4.00e+02 3.23e-02 1.67e+00 pdb=" N PRO m 368 " 0.056 5.00e-02 4.00e+02 pdb=" CA PRO m 368 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO m 368 " -0.018 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL m 265 " 0.020 5.00e-02 4.00e+02 3.10e-02 1.54e+00 pdb=" N PRO m 266 " -0.054 5.00e-02 4.00e+02 pdb=" CA PRO m 266 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO m 266 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA SER m 94 " -0.006 2.00e-02 2.50e+03 1.19e-02 1.43e+00 pdb=" C SER m 94 " 0.021 2.00e-02 2.50e+03 pdb=" O SER m 94 " -0.008 2.00e-02 2.50e+03 pdb=" N ALA m 95 " -0.007 2.00e-02 2.50e+03 ... (remaining 638 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.69: 58 2.69 - 3.30: 3951 3.30 - 3.92: 6727 3.92 - 4.53: 8526 4.53 - 5.14: 12973 Nonbonded interactions: 32235 Sorted by model distance: nonbonded pdb="MG MG m 501 " pdb=" O3B GDP m 503 " model vdw 2.081 2.170 nonbonded pdb=" OG SER m 329 " pdb="MG MG m 501 " model vdw 2.147 2.170 nonbonded pdb=" O GLY m 348 " pdb=" NZ LYS m 351 " model vdw 2.354 3.120 nonbonded pdb=" OE1 GLU m 200 " pdb=" OG1 THR m 394 " model vdw 2.393 3.040 nonbonded pdb=" O ARG m 304 " pdb=" OE1 GLN m 308 " model vdw 2.395 3.040 ... (remaining 32230 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.820 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: 0.010 Extract box with map and model: 0.110 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.630 Find NCS groups from input model: 0.020 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:6.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7204 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 : 0.002 0.022 3745 Z= 0.113 Angle : 0.504 5.912 5049 Z= 0.261 Chirality : 0.040 0.143 550 Planarity : 0.004 0.032 641 Dihedral : 14.421 86.832 1448 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % 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: 1.73 (0.40), residues: 446 helix: 1.85 (0.38), residues: 195 sheet: 0.30 (0.82), residues: 35 loop : 0.80 (0.42), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG m 210 TYR 0.012 0.001 TYR m 323 PHE 0.006 0.001 PHE m 38 TRP 0.009 0.001 TRP m 353 HIS 0.004 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00247 ( 3745) covalent geometry : angle 0.50382 ( 5049) hydrogen bonds : bond 0.18764 ( 164) hydrogen bonds : angle 5.92233 ( 450) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.108 Fit side-chains REVERT: m 133 ASP cc_start: 0.6348 (p0) cc_final: 0.6098 (p0) REVERT: m 139 ASP cc_start: 0.6508 (m-30) cc_final: 0.6123 (m-30) REVERT: m 209 LYS cc_start: 0.6881 (mmpt) cc_final: 0.6438 (mmmt) REVERT: m 349 GLU cc_start: 0.6755 (tp30) cc_final: 0.6426 (tp30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.8236 time to fit residues: 55.5150 Evaluate side-chains 53 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 53 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 24 optimal weight: 8.9990 chunk 26 optimal weight: 0.9990 chunk 2 optimal weight: 10.0000 chunk 16 optimal weight: 8.9990 chunk 32 optimal weight: 2.9990 chunk 31 optimal weight: 7.9990 chunk 25 optimal weight: 6.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 22 optimal weight: 8.9990 chunk 37 optimal weight: 6.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 100 GLN m 213 ASN ** m 254 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 = 0.3724 r_free = 0.3724 target = 0.161966 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 63)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.137932 restraints weight = 4739.686| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.33 r_work: 0.3340 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3253 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3253 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1105 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3745 Z= 0.137 Angle : 0.536 6.247 5049 Z= 0.273 Chirality : 0.042 0.142 550 Planarity : 0.004 0.039 641 Dihedral : 5.925 80.988 505 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 3.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 2.01 % Allowed : 9.77 % Favored : 88.22 % 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: 1.78 (0.39), residues: 446 helix: 1.88 (0.38), residues: 202 sheet: 0.27 (0.83), residues: 35 loop : 0.81 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG m 151 TYR 0.010 0.002 TYR m 323 PHE 0.009 0.002 PHE m 78 TRP 0.011 0.001 TRP m 212 HIS 0.005 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3745) covalent geometry : angle 0.53575 ( 5049) hydrogen bonds : bond 0.04550 ( 164) hydrogen bonds : angle 4.65098 ( 450) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 56 time to evaluate : 0.148 Fit side-chains REVERT: m 139 ASP cc_start: 0.7087 (m-30) cc_final: 0.6767 (m-30) REVERT: m 162 LYS cc_start: 0.7386 (tttm) cc_final: 0.6996 (ttmt) REVERT: m 209 LYS cc_start: 0.6859 (mmpt) cc_final: 0.6438 (mmmt) REVERT: m 280 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7254 (mt-10) REVERT: m 349 GLU cc_start: 0.7280 (tp30) cc_final: 0.6831 (tp30) REVERT: m 410 LYS cc_start: 0.7132 (OUTLIER) cc_final: 0.6836 (ptpp) outliers start: 8 outliers final: 1 residues processed: 62 average time/residue: 0.7256 time to fit residues: 46.1070 Evaluate side-chains 54 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 51 time to evaluate : 0.156 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 280 GLU Chi-restraints excluded: chain m residue 410 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 5.9990 chunk 10 optimal weight: 5.9990 chunk 8 optimal weight: 7.9990 chunk 28 optimal weight: 5.9990 chunk 34 optimal weight: 9.9990 chunk 27 optimal weight: 10.0000 chunk 11 optimal weight: 0.7980 chunk 2 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 overall best weight: 3.5588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 100 GLN m 111 ASN m 213 ASN ** m 254 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.160825 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3425 r_free = 0.3425 target = 0.136727 restraints weight = 4738.714| |-----------------------------------------------------------------------------| r_work (start): 0.3412 rms_B_bonded: 1.33 r_work: 0.3322 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3745 Z= 0.135 Angle : 0.521 6.344 5049 Z= 0.266 Chirality : 0.042 0.141 550 Planarity : 0.004 0.040 641 Dihedral : 6.042 83.338 505 Min Nonbonded Distance : 1.989 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.51 % Allowed : 12.28 % Favored : 85.21 % 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: 1.65 (0.39), residues: 446 helix: 1.88 (0.38), residues: 202 sheet: -0.02 (0.81), residues: 35 loop : 0.65 (0.40), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG m 151 TYR 0.009 0.002 TYR m 323 PHE 0.009 0.001 PHE m 38 TRP 0.012 0.001 TRP m 212 HIS 0.005 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 3745) covalent geometry : angle 0.52091 ( 5049) hydrogen bonds : bond 0.04272 ( 164) hydrogen bonds : angle 4.53374 ( 450) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 55 time to evaluate : 0.095 Fit side-chains REVERT: m 27 GLU cc_start: 0.7659 (OUTLIER) cc_final: 0.7256 (pt0) REVERT: m 93 ARG cc_start: 0.6656 (OUTLIER) cc_final: 0.5761 (tpp-160) REVERT: m 111 ASN cc_start: 0.6326 (m-40) cc_final: 0.5534 (p0) REVERT: m 139 ASP cc_start: 0.7051 (m-30) cc_final: 0.6696 (m-30) REVERT: m 162 LYS cc_start: 0.7387 (tttm) cc_final: 0.6899 (ttmt) REVERT: m 248 LYS cc_start: 0.7686 (tttp) cc_final: 0.7151 (tmmt) REVERT: m 280 GLU cc_start: 0.7425 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: m 349 GLU cc_start: 0.7324 (tp30) cc_final: 0.6923 (tp30) outliers start: 10 outliers final: 1 residues processed: 60 average time/residue: 0.7367 time to fit residues: 45.2179 Evaluate side-chains 56 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 52 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 27 GLU Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 280 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 2.9990 chunk 38 optimal weight: 10.0000 chunk 29 optimal weight: 9.9990 chunk 13 optimal weight: 0.7980 chunk 16 optimal weight: 8.9990 chunk 26 optimal weight: 7.9990 chunk 41 optimal weight: 9.9990 chunk 27 optimal weight: 0.9980 chunk 31 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 21 optimal weight: 6.9990 overall best weight: 3.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 100 GLN m 213 ASN ** m 254 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 = 0.3707 r_free = 0.3707 target = 0.160518 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3423 r_free = 0.3423 target = 0.136560 restraints weight = 4729.824| |-----------------------------------------------------------------------------| r_work (start): 0.3409 rms_B_bonded: 1.31 r_work: 0.3318 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3231 rms_B_bonded: 3.59 restraints_weight: 0.2500 r_work (final): 0.3231 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7473 moved from start: 0.1458 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3745 Z= 0.142 Angle : 0.526 6.400 5049 Z= 0.269 Chirality : 0.042 0.136 550 Planarity : 0.004 0.042 641 Dihedral : 6.166 86.276 505 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer: Outliers : 1.75 % Allowed : 13.28 % Favored : 84.96 % 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: 1.55 (0.39), residues: 446 helix: 1.86 (0.37), residues: 202 sheet: -0.16 (0.81), residues: 35 loop : 0.56 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG m 151 TYR 0.009 0.002 TYR m 216 PHE 0.010 0.002 PHE m 38 TRP 0.012 0.001 TRP m 212 HIS 0.005 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00331 ( 3745) covalent geometry : angle 0.52557 ( 5049) hydrogen bonds : bond 0.04280 ( 164) hydrogen bonds : angle 4.50070 ( 450) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 55 time to evaluate : 0.093 Fit side-chains REVERT: m 27 GLU cc_start: 0.7698 (OUTLIER) cc_final: 0.7297 (pt0) REVERT: m 93 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5867 (tpp-160) REVERT: m 111 ASN cc_start: 0.6284 (m-40) cc_final: 0.5537 (p0) REVERT: m 139 ASP cc_start: 0.7056 (m-30) cc_final: 0.6705 (m-30) REVERT: m 248 LYS cc_start: 0.7705 (tttp) cc_final: 0.7167 (tmmt) REVERT: m 280 GLU cc_start: 0.7490 (OUTLIER) cc_final: 0.7231 (mt-10) REVERT: m 349 GLU cc_start: 0.7360 (tp30) cc_final: 0.7008 (tp30) REVERT: m 413 GLU cc_start: 0.7123 (mt-10) cc_final: 0.6876 (mt-10) outliers start: 7 outliers final: 1 residues processed: 58 average time/residue: 0.7821 time to fit residues: 46.3721 Evaluate side-chains 55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 51 time to evaluate : 0.158 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 27 GLU Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 280 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 40 optimal weight: 5.9990 chunk 30 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 1 optimal weight: 7.9990 chunk 15 optimal weight: 10.0000 chunk 4 optimal weight: 0.0570 chunk 41 optimal weight: 0.8980 chunk 18 optimal weight: 8.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 overall best weight: 3.7904 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 100 GLN m 213 ASN ** m 254 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 = 0.3705 r_free = 0.3705 target = 0.160393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3420 r_free = 0.3420 target = 0.136416 restraints weight = 4660.352| |-----------------------------------------------------------------------------| r_work (start): 0.3402 rms_B_bonded: 1.31 r_work: 0.3312 rms_B_bonded: 2.07 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 3.55 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.1541 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3745 Z= 0.138 Angle : 0.542 8.595 5049 Z= 0.269 Chirality : 0.042 0.148 550 Planarity : 0.004 0.043 641 Dihedral : 6.125 85.379 505 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 2.76 % Allowed : 14.04 % Favored : 83.21 % 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: 1.54 (0.39), residues: 446 helix: 1.90 (0.37), residues: 202 sheet: -0.30 (0.80), residues: 35 loop : 0.51 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.001 ARG m 433 TYR 0.008 0.001 TYR m 216 PHE 0.009 0.001 PHE m 38 TRP 0.012 0.001 TRP m 212 HIS 0.005 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00320 ( 3745) covalent geometry : angle 0.54240 ( 5049) hydrogen bonds : bond 0.04150 ( 164) hydrogen bonds : angle 4.48031 ( 450) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 51 time to evaluate : 0.147 Fit side-chains REVERT: m 27 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7316 (pt0) REVERT: m 93 ARG cc_start: 0.6701 (OUTLIER) cc_final: 0.5837 (tpp-160) REVERT: m 111 ASN cc_start: 0.6244 (m-40) cc_final: 0.5638 (p0) REVERT: m 139 ASP cc_start: 0.7030 (m-30) cc_final: 0.6682 (m-30) REVERT: m 248 LYS cc_start: 0.7700 (tttp) cc_final: 0.7159 (tmmt) REVERT: m 280 GLU cc_start: 0.7477 (OUTLIER) cc_final: 0.7220 (mt-10) REVERT: m 349 GLU cc_start: 0.7348 (tp30) cc_final: 0.6919 (tp30) outliers start: 11 outliers final: 2 residues processed: 56 average time/residue: 0.7780 time to fit residues: 44.5977 Evaluate side-chains 55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.191 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 27 GLU Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 280 GLU Chi-restraints excluded: chain m residue 311 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 8.9990 chunk 2 optimal weight: 7.9990 chunk 5 optimal weight: 0.0770 chunk 35 optimal weight: 1.9990 chunk 11 optimal weight: 20.0000 chunk 19 optimal weight: 2.9990 chunk 9 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 15 optimal weight: 7.9990 chunk 13 optimal weight: 7.9990 chunk 43 optimal weight: 9.9990 overall best weight: 2.8146 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 100 GLN m 213 ASN ** m 254 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 = 0.3715 r_free = 0.3715 target = 0.161308 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3428 r_free = 0.3428 target = 0.137074 restraints weight = 4740.970| |-----------------------------------------------------------------------------| r_work (start): 0.3418 rms_B_bonded: 1.34 r_work: 0.3329 rms_B_bonded: 2.08 restraints_weight: 0.5000 r_work: 0.3240 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3240 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1570 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 3745 Z= 0.115 Angle : 0.503 7.600 5049 Z= 0.249 Chirality : 0.041 0.134 550 Planarity : 0.004 0.042 641 Dihedral : 5.836 79.434 505 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.50 % Allowed : 15.54 % Favored : 82.96 % 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: 1.62 (0.39), residues: 446 helix: 1.99 (0.37), residues: 202 sheet: -0.38 (0.79), residues: 35 loop : 0.56 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 93 TYR 0.007 0.001 TYR m 171 PHE 0.007 0.001 PHE m 38 TRP 0.012 0.001 TRP m 212 HIS 0.004 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00262 ( 3745) covalent geometry : angle 0.50290 ( 5049) hydrogen bonds : bond 0.03726 ( 164) hydrogen bonds : angle 4.35418 ( 450) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 50 time to evaluate : 0.147 Fit side-chains REVERT: m 70 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7133 (mtp85) REVERT: m 93 ARG cc_start: 0.6699 (OUTLIER) cc_final: 0.5890 (tpp-160) REVERT: m 111 ASN cc_start: 0.6151 (m-40) cc_final: 0.5588 (p0) REVERT: m 139 ASP cc_start: 0.7048 (m-30) cc_final: 0.6734 (m-30) REVERT: m 248 LYS cc_start: 0.7725 (tttp) cc_final: 0.7169 (tmmt) REVERT: m 280 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: m 349 GLU cc_start: 0.7339 (tp30) cc_final: 0.6940 (tp30) outliers start: 6 outliers final: 2 residues processed: 54 average time/residue: 0.7620 time to fit residues: 42.1437 Evaluate side-chains 54 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 50 time to evaluate : 0.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 280 GLU Chi-restraints excluded: chain m residue 311 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 0.0470 chunk 34 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 39 optimal weight: 9.9990 chunk 26 optimal weight: 9.9990 chunk 40 optimal weight: 6.9990 chunk 5 optimal weight: 8.9990 chunk 15 optimal weight: 8.9990 chunk 19 optimal weight: 3.9990 chunk 4 optimal weight: 0.9980 chunk 16 optimal weight: 5.9990 overall best weight: 3.6084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 100 GLN m 213 ASN ** m 254 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 = 0.3700 r_free = 0.3700 target = 0.160053 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3410 r_free = 0.3410 target = 0.135738 restraints weight = 4804.587| |-----------------------------------------------------------------------------| r_work (start): 0.3411 rms_B_bonded: 1.35 r_work: 0.3322 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.3233 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.3233 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3745 Z= 0.133 Angle : 0.530 7.299 5049 Z= 0.264 Chirality : 0.042 0.138 550 Planarity : 0.004 0.043 641 Dihedral : 6.025 82.607 505 Min Nonbonded Distance : 1.981 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.67 % Favored : 99.33 % Rotamer: Outliers : 2.01 % Allowed : 15.29 % Favored : 82.71 % 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: 1.57 (0.39), residues: 446 helix: 1.94 (0.37), residues: 202 sheet: -0.38 (0.79), residues: 35 loop : 0.54 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 93 TYR 0.008 0.001 TYR m 216 PHE 0.009 0.001 PHE m 38 TRP 0.012 0.002 TRP m 212 HIS 0.005 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00308 ( 3745) covalent geometry : angle 0.53049 ( 5049) hydrogen bonds : bond 0.04055 ( 164) hydrogen bonds : angle 4.42878 ( 450) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 49 time to evaluate : 0.132 Fit side-chains REVERT: m 27 GLU cc_start: 0.7739 (OUTLIER) cc_final: 0.7345 (pt0) REVERT: m 93 ARG cc_start: 0.6773 (OUTLIER) cc_final: 0.5901 (tpp-160) REVERT: m 111 ASN cc_start: 0.6220 (m-40) cc_final: 0.5601 (p0) REVERT: m 139 ASP cc_start: 0.7054 (m-30) cc_final: 0.6715 (m-30) REVERT: m 248 LYS cc_start: 0.7687 (tttp) cc_final: 0.7154 (tmmt) REVERT: m 280 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.7171 (mt-10) REVERT: m 349 GLU cc_start: 0.7283 (tp30) cc_final: 0.6905 (tp30) outliers start: 8 outliers final: 2 residues processed: 53 average time/residue: 0.7883 time to fit residues: 42.8550 Evaluate side-chains 54 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 49 time to evaluate : 0.154 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 27 GLU Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 280 GLU Chi-restraints excluded: chain m residue 311 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 4 optimal weight: 20.0000 chunk 27 optimal weight: 10.0000 chunk 2 optimal weight: 7.9990 chunk 42 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 13 optimal weight: 3.9990 chunk 34 optimal weight: 9.9990 chunk 8 optimal weight: 9.9990 chunk 44 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 22 optimal weight: 5.9990 overall best weight: 3.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 100 GLN m 213 ASN ** m 254 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 = 0.3708 r_free = 0.3708 target = 0.160788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3447 r_free = 0.3447 target = 0.138637 restraints weight = 4751.881| |-----------------------------------------------------------------------------| r_work (start): 0.3431 rms_B_bonded: 1.46 r_work: 0.3324 rms_B_bonded: 1.99 restraints_weight: 0.5000 r_work: 0.3238 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.3238 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7462 moved from start: 0.1651 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3745 Z= 0.123 Angle : 0.516 6.987 5049 Z= 0.256 Chirality : 0.041 0.134 550 Planarity : 0.004 0.042 641 Dihedral : 5.944 81.411 505 Min Nonbonded Distance : 1.983 Molprobity Statistics. All-atom Clashscore : 2.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.75 % Allowed : 15.54 % Favored : 82.71 % 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: 1.62 (0.39), residues: 446 helix: 1.99 (0.37), residues: 202 sheet: -0.39 (0.79), residues: 35 loop : 0.55 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 93 TYR 0.007 0.001 TYR m 171 PHE 0.008 0.001 PHE m 38 TRP 0.012 0.001 TRP m 212 HIS 0.004 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00284 ( 3745) covalent geometry : angle 0.51596 ( 5049) hydrogen bonds : bond 0.03858 ( 164) hydrogen bonds : angle 4.38318 ( 450) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 50 time to evaluate : 0.163 Fit side-chains REVERT: m 27 GLU cc_start: 0.7695 (OUTLIER) cc_final: 0.7303 (pt0) REVERT: m 70 ARG cc_start: 0.7632 (mtt-85) cc_final: 0.7116 (mtp85) REVERT: m 93 ARG cc_start: 0.6767 (OUTLIER) cc_final: 0.5946 (tpp-160) REVERT: m 109 ARG cc_start: 0.5991 (mtt90) cc_final: 0.5668 (mtp180) REVERT: m 111 ASN cc_start: 0.6226 (m-40) cc_final: 0.5633 (p0) REVERT: m 139 ASP cc_start: 0.7050 (m-30) cc_final: 0.6740 (m-30) REVERT: m 248 LYS cc_start: 0.7743 (tttp) cc_final: 0.7189 (tmmt) REVERT: m 280 GLU cc_start: 0.7404 (OUTLIER) cc_final: 0.7167 (mt-10) REVERT: m 349 GLU cc_start: 0.7347 (tp30) cc_final: 0.6963 (tp30) outliers start: 7 outliers final: 2 residues processed: 54 average time/residue: 0.7360 time to fit residues: 40.7636 Evaluate side-chains 55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 50 time to evaluate : 0.185 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 27 GLU Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 280 GLU Chi-restraints excluded: chain m residue 311 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 5 optimal weight: 6.9990 chunk 3 optimal weight: 7.9990 chunk 29 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 37 optimal weight: 7.9990 chunk 39 optimal weight: 9.9990 chunk 14 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 17 optimal weight: 10.0000 chunk 4 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 overall best weight: 3.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 100 GLN m 213 ASN ** m 254 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 = 0.3705 r_free = 0.3705 target = 0.160628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 62)----------------| | r_work = 0.3422 r_free = 0.3422 target = 0.136692 restraints weight = 4744.457| |-----------------------------------------------------------------------------| r_work (start): 0.3413 rms_B_bonded: 1.32 r_work: 0.3323 rms_B_bonded: 2.04 restraints_weight: 0.5000 r_work: 0.3234 rms_B_bonded: 3.56 restraints_weight: 0.2500 r_work (final): 0.3234 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7468 moved from start: 0.1679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3745 Z= 0.127 Angle : 0.530 6.882 5049 Z= 0.263 Chirality : 0.042 0.144 550 Planarity : 0.004 0.043 641 Dihedral : 5.974 81.658 505 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.75 % Allowed : 16.29 % Favored : 81.95 % 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: 1.59 (0.39), residues: 446 helix: 1.97 (0.37), residues: 202 sheet: -0.40 (0.79), residues: 35 loop : 0.54 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 93 TYR 0.008 0.001 TYR m 171 PHE 0.009 0.001 PHE m 38 TRP 0.012 0.001 TRP m 212 HIS 0.004 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00295 ( 3745) covalent geometry : angle 0.52970 ( 5049) hydrogen bonds : bond 0.03952 ( 164) hydrogen bonds : angle 4.40365 ( 450) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 48 time to evaluate : 0.144 Fit side-chains REVERT: m 27 GLU cc_start: 0.7720 (OUTLIER) cc_final: 0.7326 (pt0) REVERT: m 70 ARG cc_start: 0.7638 (mtt-85) cc_final: 0.7121 (mtp85) REVERT: m 93 ARG cc_start: 0.6772 (OUTLIER) cc_final: 0.5911 (tpp-160) REVERT: m 111 ASN cc_start: 0.6215 (m-40) cc_final: 0.5497 (p0) REVERT: m 139 ASP cc_start: 0.7063 (m-30) cc_final: 0.6755 (m-30) REVERT: m 248 LYS cc_start: 0.7685 (tttp) cc_final: 0.7162 (tmmt) REVERT: m 280 GLU cc_start: 0.7426 (OUTLIER) cc_final: 0.7188 (mt-10) REVERT: m 349 GLU cc_start: 0.7364 (tp30) cc_final: 0.6980 (tp30) outliers start: 7 outliers final: 2 residues processed: 52 average time/residue: 0.7899 time to fit residues: 42.0666 Evaluate side-chains 53 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 48 time to evaluate : 0.151 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 27 GLU Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 280 GLU Chi-restraints excluded: chain m residue 311 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 11 optimal weight: 0.4980 chunk 34 optimal weight: 0.0470 chunk 5 optimal weight: 5.9990 chunk 38 optimal weight: 7.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.6980 chunk 21 optimal weight: 7.9990 chunk 2 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 29 optimal weight: 2.9990 chunk 0 optimal weight: 20.0000 overall best weight: 1.0080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 100 GLN m 213 ASN ** m 254 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 = 0.3738 r_free = 0.3738 target = 0.163616 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3482 r_free = 0.3482 target = 0.141077 restraints weight = 4848.400| |-----------------------------------------------------------------------------| r_work (start): 0.3475 rms_B_bonded: 1.55 r_work: 0.3331 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3237 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3237 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 moved from start: 0.1783 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 3745 Z= 0.085 Angle : 0.466 6.718 5049 Z= 0.227 Chirality : 0.040 0.136 550 Planarity : 0.004 0.040 641 Dihedral : 5.110 63.546 505 Min Nonbonded Distance : 2.059 Molprobity Statistics. All-atom Clashscore : 2.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.90 % Favored : 99.10 % Rotamer: Outliers : 0.75 % Allowed : 18.05 % Favored : 81.20 % 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: 1.92 (0.39), residues: 446 helix: 2.24 (0.38), residues: 202 sheet: -0.47 (0.77), residues: 35 loop : 0.76 (0.41), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 151 TYR 0.007 0.001 TYR m 171 PHE 0.006 0.001 PHE m 427 TRP 0.012 0.001 TRP m 212 HIS 0.002 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00186 ( 3745) covalent geometry : angle 0.46597 ( 5049) hydrogen bonds : bond 0.02828 ( 164) hydrogen bonds : angle 4.07279 ( 450) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 892 Ramachandran restraints generated. 446 Oldfield, 0 Emsley, 446 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 48 time to evaluate : 0.157 Fit side-chains REVERT: m 8 LYS cc_start: 0.5972 (mmmt) cc_final: 0.5454 (mptt) REVERT: m 70 ARG cc_start: 0.7675 (mtt-85) cc_final: 0.7180 (mtp85) REVERT: m 93 ARG cc_start: 0.6961 (OUTLIER) cc_final: 0.6175 (tpp-160) REVERT: m 109 ARG cc_start: 0.5985 (mtt90) cc_final: 0.5763 (mtp180) REVERT: m 111 ASN cc_start: 0.6317 (m-40) cc_final: 0.5724 (p0) REVERT: m 139 ASP cc_start: 0.7120 (m-30) cc_final: 0.6852 (m-30) REVERT: m 210 ARG cc_start: 0.7385 (OUTLIER) cc_final: 0.7139 (ttp-110) REVERT: m 346 ILE cc_start: 0.7769 (pt) cc_final: 0.7487 (mp) REVERT: m 349 GLU cc_start: 0.7393 (tp30) cc_final: 0.6960 (tp30) REVERT: m 377 ASP cc_start: 0.4868 (m-30) cc_final: 0.4519 (p0) outliers start: 3 outliers final: 1 residues processed: 51 average time/residue: 0.7656 time to fit residues: 40.0704 Evaluate side-chains 50 residues out of total 399 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 47 time to evaluate : 0.236 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain m residue 64 SER Chi-restraints excluded: chain m residue 93 ARG Chi-restraints excluded: chain m residue 210 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 45 random chunks: chunk 35 optimal weight: 0.8980 chunk 16 optimal weight: 20.0000 chunk 21 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 5 optimal weight: 8.9990 chunk 24 optimal weight: 4.9990 chunk 14 optimal weight: 0.7980 chunk 27 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 40 optimal weight: 10.0000 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: m 213 ASN ** m 254 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 = 0.3728 r_free = 0.3728 target = 0.162819 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3466 r_free = 0.3466 target = 0.139918 restraints weight = 4747.893| |-----------------------------------------------------------------------------| r_work (start): 0.3448 rms_B_bonded: 1.46 r_work: 0.3317 rms_B_bonded: 2.47 restraints_weight: 0.5000 r_work: 0.3226 rms_B_bonded: 4.25 restraints_weight: 0.2500 r_work (final): 0.3226 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7457 moved from start: 0.1757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 3745 Z= 0.096 Angle : 0.485 6.787 5049 Z= 0.236 Chirality : 0.040 0.132 550 Planarity : 0.004 0.040 641 Dihedral : 5.223 67.609 505 Min Nonbonded Distance : 2.023 Molprobity Statistics. All-atom Clashscore : 2.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 1.75 % Allowed : 17.29 % Favored : 80.95 % 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: 1.97 (0.39), residues: 446 helix: 2.26 (0.37), residues: 202 sheet: -0.46 (0.77), residues: 35 loop : 0.82 (0.42), residues: 209 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG m 93 TYR 0.006 0.001 TYR m 171 PHE 0.006 0.001 PHE m 92 TRP 0.012 0.001 TRP m 212 HIS 0.002 0.001 HIS m 287 Details of bonding type rmsd covalent geometry : bond 0.00219 ( 3745) covalent geometry : angle 0.48466 ( 5049) hydrogen bonds : bond 0.03152 ( 164) hydrogen bonds : angle 4.09106 ( 450) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1876.15 seconds wall clock time: 32 minutes 47.02 seconds (1967.02 seconds total)