Starting phenix.real_space_refine on Wed Sep 17 03:23:58 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8ybe_39117/09_2025/8ybe_39117.cif Found real_map, /net/cci-nas-00/data/ceres_data/8ybe_39117/09_2025/8ybe_39117.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8ybe_39117/09_2025/8ybe_39117.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8ybe_39117/09_2025/8ybe_39117.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8ybe_39117/09_2025/8ybe_39117.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8ybe_39117/09_2025/8ybe_39117.map" } resolution = 2.3 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= 0.018 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 6 5.16 5 C 1873 2.51 5 N 473 2.21 5 O 758 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 3110 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2890 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 370, 2879 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} Conformer: "B" Number of residues, atoms: 370, 2879 Classifications: {'peptide': 370} Link IDs: {'PTRANS': 21, 'TRANS': 348} bond proxies already assigned to first conformer: 2936 Chain: "B" Number of atoms: 23 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 23 Unusual residues: {'GLC': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "A" Number of atoms: 197 Number of conformers: 1 Conformer: "" Number of residues, atoms: 197, 197 Classifications: {'water': 197} Link IDs: {None: 196} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AARG A 393 " occ=0.50 ... (20 atoms not shown) pdb=" NH2BARG A 393 " occ=0.50 Time building chain proxies: 1.30, per 1000 atoms: 0.42 Number of scatterers: 3110 At special positions: 0 Unit cell: (50.0692, 62.7628, 77.572, 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 6 16.00 O 758 8.00 N 473 7.00 C 1873 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 Links applied ALPHA1-4 " GLC B 1 " - " GLC B 2 " Time building additional restraints: 0.34 Conformation dependent library (CDL) restraints added in 243.8 milliseconds Enol-peptide restraints added in 715.3 nanoseconds 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 684 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 4 sheets defined 54.9% alpha, 11.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.13 Creating SS restraints... Processing helix chain 'A' and resid 42 through 58 Processing helix chain 'A' and resid 68 through 80 Proline residue: A 74 - end of helix Processing helix chain 'A' and resid 90 through 100 removed outlier: 3.716A pdb=" N GLY A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 4.574A pdb=" N GLY A 95 " --> pdb=" O ASP A 91 " (cutoff:3.500A) Processing helix chain 'A' and resid 108 through 115 Processing helix chain 'A' and resid 116 through 123 Processing helix chain 'A' and resid 157 through 168 Processing helix chain 'A' and resid 179 through 190 removed outlier: 3.768A pdb=" N THR A 183 " --> pdb=" O GLU A 179 " (cutoff:3.500A) Proline residue: A 185 - end of helix removed outlier: 4.339A pdb=" N ASP A 190 " --> pdb=" O LEU A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 211 through 227 Processing helix chain 'A' and resid 235 through 245 Processing helix chain 'A' and resid 254 through 256 No H-bonds generated for 'chain 'A' and resid 254 through 256' Processing helix chain 'A' and resid 257 through 265 Processing helix chain 'A' and resid 298 through 309 Processing helix chain 'A' and resid 312 through 323 Processing helix chain 'A' and resid 330 through 338 removed outlier: 3.795A pdb=" N GLU A 336 " --> pdb=" O SER A 332 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 353 Processing helix chain 'A' and resid 360 through 379 removed outlier: 4.457A pdb=" N ALA A 364 " --> pdb=" O PRO A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 382 through 396 Processing sheet with id=AA1, first strand: chain 'A' and resid 60 through 64 removed outlier: 6.350A pdb=" N LEU A 33 " --> pdb=" O THR A 62 " (cutoff:3.500A) removed outlier: 7.328A pdb=" N GLU A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 5.914A pdb=" N ILE A 35 " --> pdb=" O GLU A 64 " (cutoff:3.500A) removed outlier: 7.508A pdb=" N ILE A 85 " --> pdb=" O LYS A 32 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N VAL A 34 " --> pdb=" O ILE A 85 " (cutoff:3.500A) removed outlier: 7.735A pdb=" N PHE A 87 " --> pdb=" O VAL A 34 " (cutoff:3.500A) removed outlier: 6.325A pdb=" N TRP A 36 " --> pdb=" O PHE A 87 " (cutoff:3.500A) removed outlier: 8.578A pdb=" N ALA A 89 " --> pdb=" O TRP A 36 " (cutoff:3.500A) removed outlier: 5.990A pdb=" N ALA A 290 " --> pdb=" O PRO A 133 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 124 through 125 Processing sheet with id=AA3, first strand: chain 'A' and resid 171 through 173 removed outlier: 8.222A pdb=" N SER A 171 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N THR A 251 " --> pdb=" O SER A 171 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N LEU A 173 " --> pdb=" O THR A 251 " (cutoff:3.500A) removed outlier: 10.897A pdb=" N ASN A 253 " --> pdb=" O LEU A 173 " (cutoff:3.500A) removed outlier: 6.406A pdb=" N ALA A 249 " --> pdb=" O ASN A 144 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 196 through 198 removed outlier: 3.668A pdb=" N LYS A 196 " --> pdb=" O ASP A 203 " (cutoff:3.500A) 149 hydrogen bonds defined for protein. 433 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: 0.51 Time building geometry restraints manager: 0.37 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 544 1.32 - 1.44: 729 1.44 - 1.56: 1698 1.56 - 1.68: 0 1.68 - 1.81: 12 Bond restraints: 2983 Sorted by residual: bond pdb=" C ALA A 172 " pdb=" O ALA A 172 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.15e-02 7.56e+03 1.05e+01 bond pdb=" CA ARG A 380 " pdb=" C ARG A 380 " ideal model delta sigma weight residual 1.524 1.484 0.039 1.29e-02 6.01e+03 9.19e+00 bond pdb=" CA LYS A 201 " pdb=" C LYS A 201 " ideal model delta sigma weight residual 1.519 1.486 0.034 1.14e-02 7.69e+03 8.68e+00 bond pdb=" C ALA A 327 " pdb=" O ALA A 327 " ideal model delta sigma weight residual 1.234 1.202 0.032 1.22e-02 6.72e+03 6.97e+00 bond pdb=" CA LYS A 32 " pdb=" C LYS A 32 " ideal model delta sigma weight residual 1.521 1.489 0.032 1.24e-02 6.50e+03 6.66e+00 ... (remaining 2978 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.80: 3842 1.80 - 3.60: 166 3.60 - 5.40: 33 5.40 - 7.20: 6 7.20 - 9.00: 3 Bond angle restraints: 4050 Sorted by residual: angle pdb=" N PRO A 357 " pdb=" CA PRO A 357 " pdb=" C PRO A 357 " ideal model delta sigma weight residual 111.68 102.68 9.00 1.67e+00 3.59e-01 2.90e+01 angle pdb=" N SER A 296 " pdb=" CA SER A 296 " pdb=" C SER A 296 " ideal model delta sigma weight residual 109.48 116.86 -7.38 1.44e+00 4.82e-01 2.63e+01 angle pdb=" N PRO A 297 " pdb=" CA PRO A 297 " pdb=" C PRO A 297 " ideal model delta sigma weight residual 114.35 108.38 5.97 1.25e+00 6.40e-01 2.28e+01 angle pdb=" C MET A 356 " pdb=" N PRO A 357 " pdb=" CA PRO A 357 " ideal model delta sigma weight residual 120.14 115.17 4.97 1.06e+00 8.90e-01 2.20e+01 angle pdb=" O ASP A 91 " pdb=" C ASP A 91 " pdb=" N ARG A 92 " ideal model delta sigma weight residual 122.20 127.09 -4.89 1.14e+00 7.69e-01 1.84e+01 ... (remaining 4045 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.04: 1614 17.04 - 34.09: 132 34.09 - 51.13: 48 51.13 - 68.17: 16 68.17 - 85.21: 4 Dihedral angle restraints: 1814 sinusoidal: 744 harmonic: 1070 Sorted by residual: dihedral pdb=" CA ASP A 56 " pdb=" C ASP A 56 " pdb=" N THR A 57 " pdb=" CA THR A 57 " ideal model delta harmonic sigma weight residual 180.00 -164.28 -15.72 0 5.00e+00 4.00e-02 9.89e+00 dihedral pdb=" CB GLU A 137 " pdb=" CG GLU A 137 " pdb=" CD GLU A 137 " pdb=" OE1 GLU A 137 " ideal model delta sinusoidal sigma weight residual 0.00 85.21 -85.21 1 3.00e+01 1.11e-03 9.78e+00 dihedral pdb=" N GLN A 381 " pdb=" CA GLN A 381 " pdb=" CB GLN A 381 " pdb=" CG GLN A 381 " ideal model delta sinusoidal sigma weight residual -180.00 -121.35 -58.65 3 1.50e+01 4.44e-03 9.47e+00 ... (remaining 1811 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.068: 374 0.068 - 0.136: 65 0.136 - 0.204: 6 0.204 - 0.273: 0 0.273 - 0.341: 1 Chirality restraints: 446 Sorted by residual: chirality pdb=" C1 GLC B 2 " pdb=" O4 GLC B 1 " pdb=" C2 GLC B 2 " pdb=" O5 GLC B 2 " both_signs ideal model delta sigma weight residual False 2.40 2.44 -0.04 2.00e-02 2.50e+03 4.34e+00 chirality pdb=" C1 GLC B 1 " pdb=" C2 GLC B 1 " pdb=" O1 GLC B 1 " pdb=" O5 GLC B 1 " both_signs ideal model delta sigma weight residual False -2.04 -2.38 0.34 2.00e-01 2.50e+01 2.90e+00 chirality pdb=" CA MET A 347 " pdb=" N MET A 347 " pdb=" C MET A 347 " pdb=" CB MET A 347 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.80e-01 ... (remaining 443 not shown) Planarity restraints: 521 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG A 92 " -0.022 2.00e-02 2.50e+03 4.43e-02 1.97e+01 pdb=" C ARG A 92 " 0.077 2.00e-02 2.50e+03 pdb=" O ARG A 92 " -0.029 2.00e-02 2.50e+03 pdb=" N PHE A 93 " -0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 392 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.02e+00 pdb=" C THR A 392 " 0.049 2.00e-02 2.50e+03 pdb=" O THR A 392 " -0.018 2.00e-02 2.50e+03 pdb=" N AARG A 393 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 392 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.64e+00 pdb=" C THR A 392 " 0.048 2.00e-02 2.50e+03 pdb=" O THR A 392 " -0.018 2.00e-02 2.50e+03 pdb=" N BARG A 393 " -0.016 2.00e-02 2.50e+03 ... (remaining 518 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 772 2.77 - 3.30: 3381 3.30 - 3.83: 6978 3.83 - 4.37: 8256 4.37 - 4.90: 12524 Nonbonded interactions: 31911 Sorted by model distance: nonbonded pdb=" OH TYR A 193 " pdb=" OD1 ASP A 206 " model vdw 2.236 3.040 nonbonded pdb=" O VAL A 76 " pdb=" OG1 THR A 79 " model vdw 2.298 3.040 nonbonded pdb=" O HOH A 454 " pdb=" O HOH A 592 " model vdw 2.327 3.040 nonbonded pdb=" OD2 ASP A 262 " pdb=" O HOH A 401 " model vdw 2.330 3.040 nonbonded pdb=" O THR A 248 " pdb=" O HOH A 402 " model vdw 2.330 3.040 ... (remaining 31906 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.50 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: 1.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.020 Set scattering table: 0.010 Process input model: 5.730 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:6.420 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 14.120 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8076 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 : 0.006 0.042 2984 Z= 0.389 Angle : 0.890 9.000 4053 Z= 0.530 Chirality : 0.053 0.341 446 Planarity : 0.008 0.061 521 Dihedral : 15.835 85.214 1130 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 18.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.34 % Allowed : 13.38 % Favored : 84.28 % 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 aren not related in a simple way. whole: 1.36 (0.41), residues: 371 helix: 0.91 (0.33), residues: 192 sheet: 0.98 (0.79), residues: 29 loop : 1.15 (0.54), residues: 150 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 370 TYR 0.022 0.002 TYR A 181 PHE 0.013 0.002 PHE A 220 TRP 0.019 0.002 TRP A 88 HIS 0.004 0.001 HIS A 229 Details of bonding type rmsd covalent geometry : bond 0.00611 ( 2983) covalent geometry : angle 0.88797 ( 4050) hydrogen bonds : bond 0.15308 ( 149) hydrogen bonds : angle 6.09893 ( 433) link_ALPHA1-4 : bond 0.00673 ( 1) link_ALPHA1-4 : angle 2.23068 ( 3) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 51 time to evaluate : 0.128 Fit side-chains REVERT: A 29 GLU cc_start: 0.6751 (tt0) cc_final: 0.5984 (mm-30) REVERT: A 98 GLN cc_start: 0.7692 (tp40) cc_final: 0.7436 (tm-30) REVERT: A 128 LYS cc_start: 0.8154 (mtpt) cc_final: 0.7932 (mtpm) REVERT: A 197 TYR cc_start: 0.7370 (t80) cc_final: 0.6600 (t80) REVERT: A 284 PHE cc_start: 0.8597 (OUTLIER) cc_final: 0.6140 (m-10) REVERT: A 354 GLU cc_start: 0.7668 (mm-30) cc_final: 0.6670 (pm20) outliers start: 6 outliers final: 1 residues processed: 55 average time/residue: 0.7100 time to fit residues: 39.9851 Evaluate side-chains 37 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 137 GLU Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 31 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 38 ASN A 279 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.142683 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3439 r_free = 0.3439 target = 0.129754 restraints weight = 6071.036| |-----------------------------------------------------------------------------| r_work (start): 0.3414 rms_B_bonded: 1.27 r_work: 0.3312 rms_B_bonded: 2.01 restraints_weight: 0.5000 r_work: 0.3195 rms_B_bonded: 3.51 restraints_weight: 0.2500 r_work (final): 0.3195 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2984 Z= 0.201 Angle : 0.659 7.330 4053 Z= 0.350 Chirality : 0.045 0.150 446 Planarity : 0.005 0.055 521 Dihedral : 6.972 66.948 439 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 12.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.54 % Favored : 99.46 % Rotamer: Outliers : 2.34 % Allowed : 15.72 % Favored : 81.94 % 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 aren not related in a simple way. whole: 1.44 (0.42), residues: 371 helix: 0.86 (0.34), residues: 192 sheet: 0.61 (0.97), residues: 24 loop : 1.45 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 370 TYR 0.023 0.002 TYR A 181 PHE 0.012 0.002 PHE A 220 TRP 0.016 0.002 TRP A 184 HIS 0.002 0.001 HIS A 65 Details of bonding type rmsd covalent geometry : bond 0.00429 ( 2983) covalent geometry : angle 0.65783 ( 4050) hydrogen bonds : bond 0.06088 ( 149) hydrogen bonds : angle 5.63578 ( 433) link_ALPHA1-4 : bond 0.00778 ( 1) link_ALPHA1-4 : angle 1.80150 ( 3) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 40 time to evaluate : 0.072 Fit side-chains REVERT: A 29 GLU cc_start: 0.7633 (tt0) cc_final: 0.7371 (tt0) REVERT: A 98 GLN cc_start: 0.7853 (tp40) cc_final: 0.7581 (tm-30) REVERT: A 128 LYS cc_start: 0.8046 (mtpt) cc_final: 0.7830 (mtpm) outliers start: 6 outliers final: 1 residues processed: 45 average time/residue: 0.6505 time to fit residues: 30.0109 Evaluate side-chains 36 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 35 time to evaluate : 0.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 10 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 36 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 1.9990 chunk 3 optimal weight: 0.5980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3581 r_free = 0.3581 target = 0.141831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.126684 restraints weight = 9020.420| |-----------------------------------------------------------------------------| r_work (start): 0.3388 rms_B_bonded: 1.65 r_work: 0.3262 rms_B_bonded: 2.50 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.27 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3116 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3116 r_free = 0.3116 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3116 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8217 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 2984 Z= 0.208 Angle : 0.642 7.308 4053 Z= 0.338 Chirality : 0.044 0.120 446 Planarity : 0.005 0.052 521 Dihedral : 5.386 52.381 436 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 12.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.36 % Favored : 98.64 % Rotamer: Outliers : 1.34 % Allowed : 15.72 % Favored : 82.94 % 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 aren not related in a simple way. whole: 1.41 (0.44), residues: 371 helix: 0.80 (0.35), residues: 192 sheet: 0.10 (1.00), residues: 24 loop : 1.59 (0.56), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.019 0.002 TYR A 181 PHE 0.013 0.002 PHE A 243 TRP 0.018 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00452 ( 2983) covalent geometry : angle 0.64033 ( 4050) hydrogen bonds : bond 0.05908 ( 149) hydrogen bonds : angle 5.67575 ( 433) link_ALPHA1-4 : bond 0.00549 ( 1) link_ALPHA1-4 : angle 1.67196 ( 3) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.126 Fit side-chains REVERT: A 29 GLU cc_start: 0.7738 (tt0) cc_final: 0.7525 (tt0) REVERT: A 98 GLN cc_start: 0.7921 (tp40) cc_final: 0.7599 (tm-30) REVERT: A 128 LYS cc_start: 0.8023 (mtpt) cc_final: 0.7813 (mtpm) REVERT: A 284 PHE cc_start: 0.8706 (OUTLIER) cc_final: 0.5978 (m-10) REVERT: A 317 GLU cc_start: 0.7994 (OUTLIER) cc_final: 0.7747 (tt0) REVERT: A 321 LYS cc_start: 0.8042 (mptp) cc_final: 0.7405 (tttm) REVERT: A 354 GLU cc_start: 0.8038 (mm-30) cc_final: 0.7013 (pm20) outliers start: 3 outliers final: 0 residues processed: 40 average time/residue: 0.6799 time to fit residues: 27.9274 Evaluate side-chains 37 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 35 time to evaluate : 0.077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 317 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 0.0770 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 24 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 8 optimal weight: 0.8980 chunk 34 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 7 optimal weight: 0.7980 chunk 15 optimal weight: 0.5980 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3613 r_free = 0.3613 target = 0.144759 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3456 r_free = 0.3456 target = 0.131268 restraints weight = 6479.639| |-----------------------------------------------------------------------------| r_work (start): 0.3455 rms_B_bonded: 1.36 r_work: 0.3345 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.3227 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.3227 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3207 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3207 r_free = 0.3207 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3207 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2984 Z= 0.169 Angle : 0.594 6.730 4053 Z= 0.310 Chirality : 0.042 0.120 446 Planarity : 0.005 0.049 521 Dihedral : 5.214 53.002 436 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 16.39 % Favored : 82.27 % 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 aren not related in a simple way. whole: 1.42 (0.44), residues: 371 helix: 0.83 (0.35), residues: 192 sheet: -0.11 (0.99), residues: 24 loop : 1.61 (0.57), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.018 0.001 TYR A 181 PHE 0.012 0.002 PHE A 243 TRP 0.016 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00364 ( 2983) covalent geometry : angle 0.59221 ( 4050) hydrogen bonds : bond 0.05293 ( 149) hydrogen bonds : angle 5.56549 ( 433) link_ALPHA1-4 : bond 0.00391 ( 1) link_ALPHA1-4 : angle 1.60022 ( 3) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 38 time to evaluate : 0.131 Fit side-chains REVERT: A 98 GLN cc_start: 0.7866 (tp40) cc_final: 0.7646 (tm-30) REVERT: A 179 GLU cc_start: 0.8392 (mm-30) cc_final: 0.8106 (mm-30) REVERT: A 317 GLU cc_start: 0.7949 (OUTLIER) cc_final: 0.7740 (tt0) REVERT: A 321 LYS cc_start: 0.7982 (mptp) cc_final: 0.7437 (tttm) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.7879 time to fit residues: 32.2531 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 317 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.0020 chunk 8 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 2 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 31 optimal weight: 0.7980 overall best weight: 0.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.145000 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3440 r_free = 0.3440 target = 0.129765 restraints weight = 11226.115| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 1.70 r_work: 0.3301 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3175 rms_B_bonded: 4.74 restraints_weight: 0.2500 r_work (final): 0.3175 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3136 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3136 r_free = 0.3136 target_work(ls_wunit_k1) = 0.106 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3136 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2984 Z= 0.169 Angle : 0.591 6.905 4053 Z= 0.306 Chirality : 0.042 0.120 446 Planarity : 0.004 0.048 521 Dihedral : 5.151 53.067 436 Min Nonbonded Distance : 2.604 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 2.01 % Allowed : 15.72 % Favored : 82.27 % 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 aren not related in a simple way. whole: 1.43 (0.45), residues: 371 helix: 0.89 (0.35), residues: 192 sheet: -0.32 (1.00), residues: 24 loop : 1.58 (0.58), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.016 0.001 TYR A 181 PHE 0.012 0.002 PHE A 243 TRP 0.016 0.002 TRP A 184 HIS 0.004 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00365 ( 2983) covalent geometry : angle 0.58970 ( 4050) hydrogen bonds : bond 0.05202 ( 149) hydrogen bonds : angle 5.54817 ( 433) link_ALPHA1-4 : bond 0.00376 ( 1) link_ALPHA1-4 : angle 1.57581 ( 3) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 46 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 41 time to evaluate : 0.127 Fit side-chains REVERT: A 27 LYS cc_start: 0.5410 (OUTLIER) cc_final: 0.4792 (mtmt) REVERT: A 32 LYS cc_start: 0.8360 (OUTLIER) cc_final: 0.8149 (mtpm) REVERT: A 98 GLN cc_start: 0.7993 (tp40) cc_final: 0.7770 (tm-30) REVERT: A 203 ASP cc_start: 0.7776 (t0) cc_final: 0.7366 (t0) REVERT: A 304 GLU cc_start: 0.8481 (tp30) cc_final: 0.8219 (tp30) REVERT: A 321 LYS cc_start: 0.8054 (OUTLIER) cc_final: 0.7519 (tttm) outliers start: 5 outliers final: 1 residues processed: 43 average time/residue: 0.6700 time to fit residues: 29.6063 Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 38 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 27 LYS Chi-restraints excluded: chain A residue 32 LYS Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 321 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.0770 chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 5 optimal weight: 0.0770 chunk 6 optimal weight: 0.5980 chunk 29 optimal weight: 1.9990 chunk 1 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 9 optimal weight: 0.5980 overall best weight: 0.4096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.147380 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3483 r_free = 0.3483 target = 0.133528 restraints weight = 6714.903| |-----------------------------------------------------------------------------| r_work (start): 0.3473 rms_B_bonded: 1.41 r_work: 0.3363 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3246 rms_B_bonded: 3.79 restraints_weight: 0.2500 r_work (final): 0.3246 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3222 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3222 r_free = 0.3222 target_work(ls_wunit_k1) = 0.112 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3222 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8125 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2984 Z= 0.151 Angle : 0.575 6.334 4053 Z= 0.295 Chirality : 0.042 0.120 446 Planarity : 0.004 0.047 521 Dihedral : 5.107 53.517 436 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.34 % Allowed : 16.72 % Favored : 81.94 % 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 aren not related in a simple way. whole: 1.38 (0.45), residues: 371 helix: 0.85 (0.35), residues: 195 sheet: -0.35 (1.00), residues: 24 loop : 1.56 (0.58), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.016 0.001 TYR A 181 PHE 0.012 0.002 PHE A 175 TRP 0.014 0.002 TRP A 184 HIS 0.003 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 2983) covalent geometry : angle 0.57373 ( 4050) hydrogen bonds : bond 0.04839 ( 149) hydrogen bonds : angle 5.45950 ( 433) link_ALPHA1-4 : bond 0.00357 ( 1) link_ALPHA1-4 : angle 1.53296 ( 3) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 41 time to evaluate : 0.145 Fit side-chains REVERT: A 92 ARG cc_start: 0.8058 (mmt180) cc_final: 0.7681 (mmm160) REVERT: A 98 GLN cc_start: 0.7865 (tp40) cc_final: 0.7653 (tm-30) REVERT: A 304 GLU cc_start: 0.8344 (tp30) cc_final: 0.8061 (tp30) REVERT: A 314 GLU cc_start: 0.7185 (mp0) cc_final: 0.6926 (mp0) REVERT: A 321 LYS cc_start: 0.7931 (mptp) cc_final: 0.7399 (tttm) outliers start: 3 outliers final: 1 residues processed: 43 average time/residue: 0.7988 time to fit residues: 35.0918 Evaluate side-chains 38 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 37 time to evaluate : 0.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 25 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 28 optimal weight: 0.9980 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.9990 chunk 12 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 15 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3604 r_free = 0.3604 target = 0.144186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3446 r_free = 0.3446 target = 0.130498 restraints weight = 6160.893| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 1.34 r_work: 0.3334 rms_B_bonded: 2.10 restraints_weight: 0.5000 r_work: 0.3219 rms_B_bonded: 3.57 restraints_weight: 0.2500 r_work (final): 0.3219 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3197 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3197 r_free = 0.3197 target_work(ls_wunit_k1) = 0.111 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3197 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8170 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2984 Z= 0.186 Angle : 0.614 7.025 4053 Z= 0.316 Chirality : 0.042 0.120 446 Planarity : 0.004 0.048 521 Dihedral : 5.254 53.177 436 Min Nonbonded Distance : 2.600 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.00 % Allowed : 16.72 % Favored : 82.27 % 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 aren not related in a simple way. whole: 1.42 (0.45), residues: 371 helix: 0.91 (0.36), residues: 192 sheet: -0.50 (1.01), residues: 24 loop : 1.57 (0.58), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.014 0.001 TYR A 181 PHE 0.013 0.002 PHE A 243 TRP 0.016 0.002 TRP A 184 HIS 0.005 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00406 ( 2983) covalent geometry : angle 0.61255 ( 4050) hydrogen bonds : bond 0.05291 ( 149) hydrogen bonds : angle 5.59150 ( 433) link_ALPHA1-4 : bond 0.00396 ( 1) link_ALPHA1-4 : angle 1.70313 ( 3) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 40 time to evaluate : 0.074 Fit side-chains REVERT: A 92 ARG cc_start: 0.8116 (mmt180) cc_final: 0.7731 (mmm160) REVERT: A 98 GLN cc_start: 0.7866 (tp40) cc_final: 0.7608 (tm-30) REVERT: A 304 GLU cc_start: 0.8340 (tp30) cc_final: 0.8083 (tp30) REVERT: A 321 LYS cc_start: 0.7902 (OUTLIER) cc_final: 0.7368 (tttm) outliers start: 2 outliers final: 1 residues processed: 41 average time/residue: 0.7527 time to fit residues: 31.5785 Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 38 time to evaluate : 0.133 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 321 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3574 r_free = 0.3574 target = 0.141651 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3424 r_free = 0.3424 target = 0.128861 restraints weight = 5292.980| |-----------------------------------------------------------------------------| r_work (start): 0.3422 rms_B_bonded: 1.20 r_work: 0.3320 rms_B_bonded: 1.88 restraints_weight: 0.5000 r_work: 0.3208 rms_B_bonded: 3.24 restraints_weight: 0.2500 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3194 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.37 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3194 r_free = 0.3194 target_work(ls_wunit_k1) = 0.110 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3194 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.1809 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2984 Z= 0.217 Angle : 0.654 7.132 4053 Z= 0.338 Chirality : 0.044 0.121 446 Planarity : 0.005 0.048 521 Dihedral : 5.397 52.720 436 Min Nonbonded Distance : 2.606 Molprobity Statistics. All-atom Clashscore : 11.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 16.72 % Favored : 81.94 % 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 aren not related in a simple way. whole: 1.33 (0.45), residues: 371 helix: 0.81 (0.36), residues: 192 sheet: -0.66 (1.01), residues: 24 loop : 1.57 (0.58), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 92 TYR 0.014 0.002 TYR A 181 PHE 0.015 0.003 PHE A 243 TRP 0.017 0.002 TRP A 184 HIS 0.006 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 2983) covalent geometry : angle 0.65234 ( 4050) hydrogen bonds : bond 0.05677 ( 149) hydrogen bonds : angle 5.72814 ( 433) link_ALPHA1-4 : bond 0.00637 ( 1) link_ALPHA1-4 : angle 1.79799 ( 3) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 37 time to evaluate : 0.176 Fit side-chains REVERT: A 98 GLN cc_start: 0.7869 (tp40) cc_final: 0.7628 (tm-30) REVERT: A 284 PHE cc_start: 0.8685 (OUTLIER) cc_final: 0.5862 (m-10) REVERT: A 321 LYS cc_start: 0.7936 (OUTLIER) cc_final: 0.7384 (tttm) REVERT: A 354 GLU cc_start: 0.7985 (OUTLIER) cc_final: 0.7648 (mm-30) outliers start: 3 outliers final: 0 residues processed: 38 average time/residue: 0.7447 time to fit residues: 28.9803 Evaluate side-chains 38 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 35 time to evaluate : 0.120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 354 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 26 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 27 optimal weight: 0.0010 chunk 33 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.142948 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3403 r_free = 0.3403 target = 0.126964 restraints weight = 9506.156| |-----------------------------------------------------------------------------| r_work (start): 0.3405 rms_B_bonded: 1.75 r_work: 0.3279 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3151 rms_B_bonded: 4.51 restraints_weight: 0.2500 r_work (final): 0.3151 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.36 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.105 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8209 moved from start: 0.1850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 2984 Z= 0.190 Angle : 0.632 6.898 4053 Z= 0.326 Chirality : 0.043 0.118 446 Planarity : 0.005 0.047 521 Dihedral : 5.347 53.103 436 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 10.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.63 % Favored : 98.37 % Rotamer: Outliers : 1.34 % Allowed : 17.06 % Favored : 81.61 % 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 aren not related in a simple way. whole: 1.34 (0.45), residues: 371 helix: 0.85 (0.36), residues: 192 sheet: -0.75 (1.00), residues: 24 loop : 1.55 (0.58), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.015 0.001 TYR A 181 PHE 0.014 0.002 PHE A 243 TRP 0.016 0.002 TRP A 184 HIS 0.005 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00416 ( 2983) covalent geometry : angle 0.63102 ( 4050) hydrogen bonds : bond 0.05376 ( 149) hydrogen bonds : angle 5.66450 ( 433) link_ALPHA1-4 : bond 0.00510 ( 1) link_ALPHA1-4 : angle 1.70366 ( 3) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 39 time to evaluate : 0.128 Fit side-chains REVERT: A 92 ARG cc_start: 0.8269 (mmt180) cc_final: 0.7807 (mmm160) REVERT: A 98 GLN cc_start: 0.7890 (tp40) cc_final: 0.7645 (tm-30) REVERT: A 237 SER cc_start: 0.8299 (m) cc_final: 0.8049 (t) REVERT: A 321 LYS cc_start: 0.7990 (OUTLIER) cc_final: 0.7386 (tttm) REVERT: A 354 GLU cc_start: 0.7953 (OUTLIER) cc_final: 0.7592 (mm-30) outliers start: 3 outliers final: 1 residues processed: 40 average time/residue: 0.7243 time to fit residues: 29.7107 Evaluate side-chains 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 321 LYS Chi-restraints excluded: chain A residue 354 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 17 optimal weight: 0.2980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 2.9990 chunk 28 optimal weight: 0.9990 chunk 12 optimal weight: 0.2980 chunk 27 optimal weight: 0.6980 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 5 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.145810 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.130685 restraints weight = 8177.471| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 1.61 r_work: 0.3324 rms_B_bonded: 2.45 restraints_weight: 0.5000 r_work: 0.3200 rms_B_bonded: 4.23 restraints_weight: 0.2500 r_work (final): 0.3200 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3177 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3177 r_free = 0.3177 target_work(ls_wunit_k1) = 0.109 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3177 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8165 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.029 2984 Z= 0.165 Angle : 0.610 7.434 4053 Z= 0.313 Chirality : 0.042 0.119 446 Planarity : 0.004 0.046 521 Dihedral : 5.243 53.296 436 Min Nonbonded Distance : 2.611 Molprobity Statistics. All-atom Clashscore : 10.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.34 % Allowed : 17.06 % Favored : 81.61 % 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 aren not related in a simple way. whole: 1.26 (0.45), residues: 371 helix: 0.81 (0.36), residues: 195 sheet: -0.91 (0.97), residues: 24 loop : 1.51 (0.59), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.015 0.001 TYR A 181 PHE 0.012 0.002 PHE A 243 TRP 0.015 0.002 TRP A 184 HIS 0.003 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00359 ( 2983) covalent geometry : angle 0.60847 ( 4050) hydrogen bonds : bond 0.05026 ( 149) hydrogen bonds : angle 5.55189 ( 433) link_ALPHA1-4 : bond 0.00426 ( 1) link_ALPHA1-4 : angle 1.60442 ( 3) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 742 Ramachandran restraints generated. 371 Oldfield, 0 Emsley, 371 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 40 time to evaluate : 0.132 Fit side-chains REVERT: A 92 ARG cc_start: 0.8214 (mmt180) cc_final: 0.7771 (mmm160) REVERT: A 98 GLN cc_start: 0.7851 (tp40) cc_final: 0.7631 (tm-30) REVERT: A 203 ASP cc_start: 0.7599 (t0) cc_final: 0.7281 (t0) REVERT: A 237 SER cc_start: 0.8256 (m) cc_final: 0.8040 (t) REVERT: A 314 GLU cc_start: 0.7243 (mp0) cc_final: 0.6971 (mp0) REVERT: A 321 LYS cc_start: 0.7934 (mptp) cc_final: 0.7335 (tttm) REVERT: A 354 GLU cc_start: 0.7834 (OUTLIER) cc_final: 0.7480 (mm-30) outliers start: 3 outliers final: 1 residues processed: 42 average time/residue: 0.7011 time to fit residues: 30.2118 Evaluate side-chains 39 residues out of total 297 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 37 time to evaluate : 0.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 284 PHE Chi-restraints excluded: chain A residue 354 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 16 optimal weight: 2.9990 chunk 1 optimal weight: 0.7980 chunk 11 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 24 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 19 optimal weight: 0.7980 chunk 7 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 279 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3591 r_free = 0.3591 target = 0.143058 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3398 r_free = 0.3398 target = 0.126645 restraints weight = 10344.047| |-----------------------------------------------------------------------------| r_work (start): 0.3400 rms_B_bonded: 1.85 r_work: 0.3271 rms_B_bonded: 2.75 restraints_weight: 0.5000 r_work: 0.3141 rms_B_bonded: 4.69 restraints_weight: 0.2500 r_work (final): 0.3141 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3121 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3121 r_free = 0.3121 target_work(ls_wunit_k1) = 0.104 | | occupancies: max = 1.00 min = 0.32 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3121 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1914 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 2984 Z= 0.200 Angle : 0.660 7.356 4053 Z= 0.338 Chirality : 0.043 0.120 446 Planarity : 0.005 0.047 521 Dihedral : 5.354 53.296 436 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 11.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.90 % Favored : 98.10 % Rotamer: Outliers : 1.34 % Allowed : 17.06 % Favored : 81.61 % 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 aren not related in a simple way. whole: 1.20 (0.45), residues: 371 helix: 0.73 (0.35), residues: 195 sheet: -0.88 (1.00), residues: 24 loop : 1.53 (0.59), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 342 TYR 0.014 0.002 TYR A 181 PHE 0.014 0.002 PHE A 243 TRP 0.017 0.002 TRP A 184 HIS 0.005 0.002 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00446 ( 2983) covalent geometry : angle 0.65869 ( 4050) hydrogen bonds : bond 0.05399 ( 149) hydrogen bonds : angle 5.62679 ( 433) link_ALPHA1-4 : bond 0.00553 ( 1) link_ALPHA1-4 : angle 1.69074 ( 3) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1619.04 seconds wall clock time: 28 minutes 26.21 seconds (1706.21 seconds total)