Starting phenix.real_space_refine on Wed Jun 3 10:06:03 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k7s_62152/06_2026/9k7s_62152.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k7s_62152/06_2026/9k7s_62152.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.69 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/9k7s_62152/06_2026/9k7s_62152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k7s_62152/06_2026/9k7s_62152.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/9k7s_62152/06_2026/9k7s_62152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k7s_62152/06_2026/9k7s_62152.map" } resolution = 3.69 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= 0.016 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 23 5.16 5 C 1990 2.51 5 N 457 2.21 5 O 499 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.00s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6079/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 2969 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2950 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2950 Classifications: {'peptide': 371} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 359} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 13 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 19 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 19 Unusual residues: {'NOS%rna2p': 1} Classifications: {'undetermined': 1} Modifications used: {'rna2p': 1} Time building chain proxies: 0.97, per 1000 atoms: 0.33 Number of scatterers: 2969 At special positions: 0 Unit cell: (73.7, 71.5, 75.9, 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 23 16.00 O 499 8.00 N 457 7.00 C 1990 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 143 " - pdb=" SG CYS A 382 " distance=2.04 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: 0.29 Conformation dependent library (CDL) restraints added in 121.3 milliseconds 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 700 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 1 sheets defined 84.4% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.09 Creating SS restraints... Processing helix chain 'A' and resid 31 through 59 removed outlier: 3.648A pdb=" N LEU A 50 " --> pdb=" O GLY A 46 " (cutoff:3.500A) removed outlier: 4.806A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 5.483A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 83 removed outlier: 4.356A pdb=" N THR A 67 " --> pdb=" O PHE A 63 " (cutoff:3.500A) removed outlier: 4.344A pdb=" N PHE A 68 " --> pdb=" O LYS A 64 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ALA A 80 " --> pdb=" O SER A 76 " (cutoff:3.500A) removed outlier: 4.410A pdb=" N LEU A 81 " --> pdb=" O SER A 77 " (cutoff:3.500A) removed outlier: 4.279A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 88 No H-bonds generated for 'chain 'A' and resid 86 through 88' Processing helix chain 'A' and resid 89 through 111 Processing helix chain 'A' and resid 112 through 143 removed outlier: 3.798A pdb=" N ILE A 125 " --> pdb=" O LEU A 121 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 172 removed outlier: 3.720A pdb=" N TYR A 152 " --> pdb=" O ASN A 148 " (cutoff:3.500A) removed outlier: 4.338A pdb=" N GLY A 161 " --> pdb=" O ILE A 157 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N VAL A 162 " --> pdb=" O GLY A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 185 through 210 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 239 through 257 removed outlier: 3.619A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN A 250 " --> pdb=" O MET A 246 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N LEU A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) removed outlier: 3.698A pdb=" N GLN A 255 " --> pdb=" O TRP A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 259 through 270 removed outlier: 3.949A pdb=" N TRP A 265 " --> pdb=" O GLY A 261 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 290 removed outlier: 3.913A pdb=" N SER A 290 " --> pdb=" O PHE A 286 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 296 Proline residue: A 294 - end of helix No H-bonds generated for 'chain 'A' and resid 291 through 296' Processing helix chain 'A' and resid 299 through 304 removed outlier: 4.057A pdb=" N ASN A 304 " --> pdb=" O LYS A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 308 through 319 Processing helix chain 'A' and resid 321 through 332 removed outlier: 3.763A pdb=" N TRP A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 365 removed outlier: 4.305A pdb=" N GLN A 343 " --> pdb=" O ASN A 339 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N TRP A 356 " --> pdb=" O PHE A 352 " (cutoff:3.500A) Proline residue: A 361 - end of helix Processing helix chain 'A' and resid 374 through 399 removed outlier: 3.619A pdb=" N ILE A 378 " --> pdb=" O LYS A 374 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N TRP A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) removed outlier: 4.104A pdb=" N THR A 399 " --> pdb=" O CYS A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 399 through 404 removed outlier: 3.831A pdb=" N TYR A 403 " --> pdb=" O THR A 399 " (cutoff:3.500A) removed outlier: 3.867A pdb=" N ASN A 404 " --> pdb=" O THR A 400 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 399 through 404' Processing sheet with id=AA1, first strand: chain 'A' and resid 179 through 180 212 hydrogen bonds defined for protein. 633 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: 0.44 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: 1.22 - 1.34: 858 1.34 - 1.46: 745 1.46 - 1.58: 1411 1.58 - 1.71: 0 1.71 - 1.83: 34 Bond restraints: 3048 Sorted by residual: bond pdb=" C3' NOS A 501 " pdb=" O3' NOS A 501 " ideal model delta sigma weight residual 1.402 1.426 -0.024 2.00e-02 2.50e+03 1.49e+00 bond pdb=" C4' NOS A 501 " pdb=" O4' NOS A 501 " ideal model delta sigma weight residual 1.432 1.454 -0.022 2.00e-02 2.50e+03 1.23e+00 bond pdb=" C1' NOS A 501 " pdb=" N9 NOS A 501 " ideal model delta sigma weight residual 1.444 1.466 -0.022 2.00e-02 2.50e+03 1.19e+00 bond pdb=" C2' NOS A 501 " pdb=" O2' NOS A 501 " ideal model delta sigma weight residual 1.390 1.411 -0.021 2.00e-02 2.50e+03 1.10e+00 bond pdb=" N VAL A 360 " pdb=" CA VAL A 360 " ideal model delta sigma weight residual 1.463 1.475 -0.012 1.20e-02 6.94e+03 1.06e+00 ... (remaining 3043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 4046 1.36 - 2.73: 75 2.73 - 4.09: 11 4.09 - 5.46: 6 5.46 - 6.82: 3 Bond angle restraints: 4141 Sorted by residual: angle pdb=" N PRO A 293 " pdb=" CA PRO A 293 " pdb=" C PRO A 293 " ideal model delta sigma weight residual 110.70 113.84 -3.14 1.22e+00 6.72e-01 6.60e+00 angle pdb=" N TYR A 292 " pdb=" CA TYR A 292 " pdb=" C TYR A 292 " ideal model delta sigma weight residual 109.81 115.32 -5.51 2.21e+00 2.05e-01 6.21e+00 angle pdb=" CA PRO A 293 " pdb=" C PRO A 293 " pdb=" N PRO A 294 " ideal model delta sigma weight residual 117.93 120.25 -2.32 1.20e+00 6.94e-01 3.75e+00 angle pdb=" CA CYS A 382 " pdb=" CB CYS A 382 " pdb=" SG CYS A 382 " ideal model delta sigma weight residual 114.40 118.57 -4.17 2.30e+00 1.89e-01 3.29e+00 angle pdb=" C ILE A 61 " pdb=" N ASN A 62 " pdb=" CA ASN A 62 " ideal model delta sigma weight residual 120.90 123.46 -2.56 1.41e+00 5.03e-01 3.29e+00 ... (remaining 4136 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.88: 1557 11.88 - 23.77: 146 23.77 - 35.65: 47 35.65 - 47.54: 11 47.54 - 59.42: 11 Dihedral angle restraints: 1772 sinusoidal: 691 harmonic: 1081 Sorted by residual: dihedral pdb=" CA CYS A 208 " pdb=" C CYS A 208 " pdb=" N ASN A 209 " pdb=" CA ASN A 209 " ideal model delta harmonic sigma weight residual -180.00 -161.42 -18.58 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA PHE A 307 " pdb=" C PHE A 307 " pdb=" N SER A 308 " pdb=" CA SER A 308 " ideal model delta harmonic sigma weight residual 180.00 162.54 17.46 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA PRO A 335 " pdb=" C PRO A 335 " pdb=" N PHE A 336 " pdb=" CA PHE A 336 " ideal model delta harmonic sigma weight residual 180.00 163.66 16.34 0 5.00e+00 4.00e-02 1.07e+01 ... (remaining 1769 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.025: 259 0.025 - 0.050: 132 0.050 - 0.075: 72 0.075 - 0.100: 18 0.100 - 0.126: 9 Chirality restraints: 490 Sorted by residual: chirality pdb=" CA ILE A 299 " pdb=" N ILE A 299 " pdb=" C ILE A 299 " pdb=" CB ILE A 299 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 chirality pdb=" CA PRO A 361 " pdb=" N PRO A 361 " pdb=" C PRO A 361 " pdb=" CB PRO A 361 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.34e-01 chirality pdb=" CA ILE A 85 " pdb=" N ILE A 85 " pdb=" C ILE A 85 " pdb=" CB ILE A 85 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.11 2.00e-01 2.50e+01 3.21e-01 ... (remaining 487 not shown) Planarity restraints: 497 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 293 " 0.026 5.00e-02 4.00e+02 3.87e-02 2.40e+00 pdb=" N PRO A 294 " -0.067 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 176 " -0.020 5.00e-02 4.00e+02 3.08e-02 1.51e+00 pdb=" N PRO A 177 " 0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 177 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 177 " -0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA CYS A 382 " 0.005 2.00e-02 2.50e+03 1.08e-02 1.17e+00 pdb=" C CYS A 382 " -0.019 2.00e-02 2.50e+03 pdb=" O CYS A 382 " 0.007 2.00e-02 2.50e+03 pdb=" N THR A 383 " 0.006 2.00e-02 2.50e+03 ... (remaining 494 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 498 2.76 - 3.30: 3002 3.30 - 3.83: 4743 3.83 - 4.37: 5324 4.37 - 4.90: 9253 Nonbonded interactions: 22820 Sorted by model distance: nonbonded pdb=" OH TYR A 65 " pdb=" OD1 ASP A 117 " model vdw 2.228 3.040 nonbonded pdb=" OD1 ASN A 54 " pdb=" NE2 GLN A 284 " model vdw 2.456 3.120 nonbonded pdb=" OD1 ASN A 51 " pdb=" OG SER A 160 " model vdw 2.461 3.040 nonbonded pdb=" O LEU A 369 " pdb=" NZ LYS A 373 " model vdw 2.489 3.120 nonbonded pdb=" NE2 GLN A 105 " pdb=" OE2 GLU A 196 " model vdw 2.499 3.120 ... (remaining 22815 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.070 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.060 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 5.080 Find NCS groups from input model: 0.010 Set up NCS constraints: 0.000 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.290 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.530 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5272 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3049 Z= 0.153 Angle : 0.518 6.819 4143 Z= 0.284 Chirality : 0.039 0.126 490 Planarity : 0.004 0.039 497 Dihedral : 11.741 59.421 1069 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 3.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 2.13 % Allowed : 6.40 % Favored : 91.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 3.00 (0.45), residues: 367 helix: 2.65 (0.30), residues: 270 sheet: None (None), residues: 0 loop : 0.06 (0.72), residues: 97 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG A 319 TYR 0.008 0.001 TYR A 240 PHE 0.009 0.001 PHE A 104 TRP 0.004 0.001 TRP A 398 HIS 0.002 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00272 / 0.15 ( 3048) covalent geometry : angle 0.51686 / 0.28 ( 4141) SS BOND : bond 0.00993 / 0.52 ( 1) SS BOND : angle 1.67762 / 0.90 ( 2) hydrogen bonds : bond 0.11719 / 8.47 ( 212) hydrogen bonds : angle 4.82255 / 3.45 ( 633) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 56 time to evaluate : 0.109 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 54 ASN cc_start: 0.4854 (m-40) cc_final: 0.4453 (m-40) REVERT: A 247 PHE cc_start: 0.6050 (t80) cc_final: 0.5832 (t80) REVERT: A 347 MET cc_start: 0.6718 (mmt) cc_final: 0.6488 (mpp) REVERT: A 408 ILE cc_start: 0.7019 (mt) cc_final: 0.6801 (mm) outliers start: 7 outliers final: 1 residues processed: 61 average time/residue: 0.0390 time to fit residues: 3.1311 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 46 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 265 TRP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 24 optimal weight: 0.9980 chunk 26 optimal weight: 0.6980 chunk 2 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 25 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 30 optimal weight: 0.2980 chunk 22 optimal weight: 0.8980 chunk 13 optimal weight: 0.7980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 105 GLN ** A 316 ASN ** 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 = 0.4561 r_free = 0.4561 target = 0.203338 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.4345 r_free = 0.4345 target = 0.181734 restraints weight = 5030.028| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.185358 restraints weight = 3441.480| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.4410 r_free = 0.4410 target = 0.187926 restraints weight = 2564.049| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.189738 restraints weight = 2045.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4441 r_free = 0.4441 target = 0.191025 restraints weight = 1712.529| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5536 moved from start: 0.2097 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 3049 Z= 0.188 Angle : 0.615 6.746 4143 Z= 0.330 Chirality : 0.041 0.146 490 Planarity : 0.004 0.045 497 Dihedral : 6.689 48.040 407 Min Nonbonded Distance : 2.559 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 5.18 % Allowed : 6.71 % Favored : 88.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.55 (0.44), residues: 367 helix: 2.38 (0.30), residues: 273 sheet: None (None), residues: 0 loop : -0.39 (0.71), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.012 0.001 TYR A 274 PHE 0.018 0.002 PHE A 283 TRP 0.010 0.002 TRP A 53 HIS 0.007 0.002 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00391 / 0.19 ( 3048) covalent geometry : angle 0.61139 / 0.33 ( 4141) SS BOND : bond 0.01456 / 0.77 ( 1) SS BOND : angle 2.89256 / 1.59 ( 2) hydrogen bonds : bond 0.07050 / 4.84 ( 212) hydrogen bonds : angle 4.18948 / 3.04 ( 633) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 53 time to evaluate : 0.116 Fit side-chains revert: symmetry clash REVERT: A 169 LEU cc_start: 0.3492 (OUTLIER) cc_final: 0.3104 (tt) REVERT: A 247 PHE cc_start: 0.6221 (t80) cc_final: 0.5979 (t80) REVERT: A 298 HIS cc_start: 0.2761 (OUTLIER) cc_final: 0.2139 (p90) REVERT: A 347 MET cc_start: 0.6605 (mmt) cc_final: 0.6068 (mmp) REVERT: A 374 LYS cc_start: 0.5008 (mttt) cc_final: 0.4473 (tptp) REVERT: A 408 ILE cc_start: 0.7045 (mt) cc_final: 0.6760 (mm) outliers start: 17 outliers final: 8 residues processed: 65 average time/residue: 0.0484 time to fit residues: 4.0516 Evaluate side-chains 56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 46 time to evaluate : 0.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 171 LEU Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 407 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 1 optimal weight: 0.6980 chunk 11 optimal weight: 0.4980 chunk 0 optimal weight: 0.7980 chunk 34 optimal weight: 0.8980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.4980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.1980 chunk 31 optimal weight: 0.0980 overall best weight: 0.3780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4557 r_free = 0.4557 target = 0.201893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4323 r_free = 0.4323 target = 0.179173 restraints weight = 5068.318| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4358 r_free = 0.4358 target = 0.182615 restraints weight = 3458.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.185546 restraints weight = 2603.825| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 40)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.187645 restraints weight = 2053.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 34)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.189047 restraints weight = 1703.341| |-----------------------------------------------------------------------------| r_work (final): 0.4400 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5602 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3049 Z= 0.171 Angle : 0.602 8.889 4143 Z= 0.317 Chirality : 0.041 0.158 490 Planarity : 0.004 0.045 497 Dihedral : 6.564 48.667 407 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.79 % Allowed : 8.84 % Favored : 85.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.25 (0.44), residues: 367 helix: 2.11 (0.30), residues: 282 sheet: None (None), residues: 0 loop : -0.62 (0.70), residues: 85 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 291 TYR 0.010 0.001 TYR A 274 PHE 0.017 0.001 PHE A 286 TRP 0.007 0.001 TRP A 398 HIS 0.006 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00343 / 0.17 ( 3048) covalent geometry : angle 0.60038 / 0.32 ( 4141) SS BOND : bond 0.01118 / 0.59 ( 1) SS BOND : angle 2.27943 / 1.25 ( 2) hydrogen bonds : bond 0.06630 / 4.54 ( 212) hydrogen bonds : angle 4.08808 / 2.99 ( 633) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 48 time to evaluate : 0.092 Fit side-chains revert: symmetry clash REVERT: A 298 HIS cc_start: 0.2669 (OUTLIER) cc_final: 0.2016 (p90) REVERT: A 347 MET cc_start: 0.6145 (mmt) cc_final: 0.5816 (mmp) REVERT: A 374 LYS cc_start: 0.5196 (mttt) cc_final: 0.4666 (tptp) REVERT: A 408 ILE cc_start: 0.7014 (mt) cc_final: 0.6762 (mm) outliers start: 19 outliers final: 10 residues processed: 58 average time/residue: 0.0491 time to fit residues: 3.6012 Evaluate side-chains 54 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 43 time to evaluate : 0.116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 407 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 28 optimal weight: 0.8980 chunk 10 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 24 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN ** A 316 ASN ** 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 = 0.4485 r_free = 0.4485 target = 0.195577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4261 r_free = 0.4261 target = 0.174757 restraints weight = 4948.820| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4299 r_free = 0.4299 target = 0.177936 restraints weight = 3493.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.180292 restraints weight = 2649.139| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4343 r_free = 0.4343 target = 0.181868 restraints weight = 2127.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.183343 restraints weight = 1802.940| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5734 moved from start: 0.3811 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 3049 Z= 0.240 Angle : 0.700 8.958 4143 Z= 0.369 Chirality : 0.044 0.148 490 Planarity : 0.004 0.043 497 Dihedral : 6.993 46.709 407 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.18 % Allowed : 12.20 % Favored : 82.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.19 (0.44), residues: 367 helix: 1.46 (0.31), residues: 291 sheet: None (None), residues: 0 loop : -1.83 (0.65), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.015 0.001 TYR A 274 PHE 0.018 0.002 PHE A 286 TRP 0.013 0.002 TRP A 53 HIS 0.009 0.002 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00524 / 0.24 ( 3048) covalent geometry : angle 0.69869 / 0.37 ( 4141) SS BOND : bond 0.01005 / 0.53 ( 1) SS BOND : angle 2.23324 / 1.19 ( 2) hydrogen bonds : bond 0.08104 / 5.57 ( 212) hydrogen bonds : angle 4.50008 / 3.32 ( 633) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 46 time to evaluate : 0.090 Fit side-chains REVERT: A 265 TRP cc_start: 0.7438 (OUTLIER) cc_final: 0.7129 (m-10) REVERT: A 298 HIS cc_start: 0.2717 (OUTLIER) cc_final: 0.1984 (p90) REVERT: A 335 PRO cc_start: 0.3448 (Cg_endo) cc_final: 0.3129 (Cg_exo) REVERT: A 374 LYS cc_start: 0.5550 (mttt) cc_final: 0.5267 (tptp) REVERT: A 381 ILE cc_start: 0.7673 (mm) cc_final: 0.7384 (mt) REVERT: A 408 ILE cc_start: 0.7126 (mt) cc_final: 0.6773 (mm) outliers start: 17 outliers final: 11 residues processed: 58 average time/residue: 0.0504 time to fit residues: 3.6940 Evaluate side-chains 60 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 407 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 1.9990 chunk 33 optimal weight: 0.0370 chunk 10 optimal weight: 0.2980 chunk 30 optimal weight: 0.0970 chunk 26 optimal weight: 0.0030 chunk 15 optimal weight: 0.6980 chunk 23 optimal weight: 0.1980 chunk 17 optimal weight: 0.6980 chunk 21 optimal weight: 0.1980 chunk 11 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 overall best weight: 0.1066 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4545 r_free = 0.4545 target = 0.202702 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.181869 restraints weight = 4837.022| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.185294 restraints weight = 3299.269| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4403 r_free = 0.4403 target = 0.187861 restraints weight = 2444.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.189741 restraints weight = 1928.321| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 44)----------------| | r_work = 0.4438 r_free = 0.4438 target = 0.191373 restraints weight = 1596.161| |-----------------------------------------------------------------------------| r_work (final): 0.4432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5554 moved from start: 0.3876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3049 Z= 0.142 Angle : 0.591 8.066 4143 Z= 0.302 Chirality : 0.040 0.170 490 Planarity : 0.004 0.041 497 Dihedral : 5.952 43.499 407 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 4.88 % Allowed : 14.02 % Favored : 81.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.82 (0.44), residues: 367 helix: 1.87 (0.31), residues: 284 sheet: None (None), residues: 0 loop : -1.11 (0.66), residues: 83 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.007 0.001 TYR A 119 PHE 0.019 0.001 PHE A 257 TRP 0.009 0.001 TRP A 356 HIS 0.002 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 ( 3048) covalent geometry : angle 0.59083 / 0.30 ( 4141) SS BOND : bond 0.00902 / 0.47 ( 1) SS BOND : angle 1.08003 / 0.58 ( 2) hydrogen bonds : bond 0.05571 / 3.79 ( 212) hydrogen bonds : angle 3.99542 / 2.93 ( 633) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 47 time to evaluate : 0.110 Fit side-chains REVERT: A 104 PHE cc_start: 0.5686 (OUTLIER) cc_final: 0.4184 (m-80) REVERT: A 169 LEU cc_start: 0.3752 (OUTLIER) cc_final: 0.3547 (tt) REVERT: A 260 VAL cc_start: 0.7585 (OUTLIER) cc_final: 0.7333 (p) REVERT: A 265 TRP cc_start: 0.7267 (OUTLIER) cc_final: 0.7052 (m-10) REVERT: A 298 HIS cc_start: 0.2568 (OUTLIER) cc_final: 0.1899 (p90) REVERT: A 326 PHE cc_start: 0.6476 (OUTLIER) cc_final: 0.4913 (m-80) REVERT: A 335 PRO cc_start: 0.3484 (Cg_endo) cc_final: 0.3244 (Cg_exo) REVERT: A 374 LYS cc_start: 0.5419 (mttt) cc_final: 0.4916 (tptp) REVERT: A 408 ILE cc_start: 0.7054 (mt) cc_final: 0.6747 (mm) outliers start: 16 outliers final: 8 residues processed: 55 average time/residue: 0.0485 time to fit residues: 3.4696 Evaluate side-chains 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 47 time to evaluate : 0.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 185 LYS Chi-restraints excluded: chain A residue 260 VAL Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 407 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 30 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 4 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 3 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 0.9990 chunk 18 optimal weight: 0.3980 chunk 33 optimal weight: 0.7980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 284 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4468 r_free = 0.4468 target = 0.194537 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.173581 restraints weight = 4809.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.176749 restraints weight = 3321.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.179084 restraints weight = 2492.716| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4327 r_free = 0.4327 target = 0.180717 restraints weight = 1991.692| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4342 r_free = 0.4342 target = 0.182156 restraints weight = 1678.376| |-----------------------------------------------------------------------------| r_work (final): 0.4343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5736 moved from start: 0.4356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 3049 Z= 0.225 Angle : 0.664 10.332 4143 Z= 0.351 Chirality : 0.043 0.132 490 Planarity : 0.004 0.044 497 Dihedral : 6.374 42.252 407 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 6.71 % Allowed : 12.80 % Favored : 80.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.12 (0.44), residues: 367 helix: 1.39 (0.31), residues: 290 sheet: None (None), residues: 0 loop : -1.71 (0.64), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.012 0.001 TYR A 274 PHE 0.022 0.002 PHE A 257 TRP 0.008 0.002 TRP A 53 HIS 0.008 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00490 / 0.23 ( 3048) covalent geometry : angle 0.66310 / 0.35 ( 4141) SS BOND : bond 0.00951 / 0.50 ( 1) SS BOND : angle 1.67414 / 0.91 ( 2) hydrogen bonds : bond 0.07653 / 5.27 ( 212) hydrogen bonds : angle 4.42560 / 3.26 ( 633) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 44 time to evaluate : 0.111 Fit side-chains REVERT: A 104 PHE cc_start: 0.5681 (OUTLIER) cc_final: 0.4093 (m-80) REVERT: A 265 TRP cc_start: 0.7377 (OUTLIER) cc_final: 0.6953 (m-10) REVERT: A 298 HIS cc_start: 0.2655 (OUTLIER) cc_final: 0.1922 (p90) REVERT: A 374 LYS cc_start: 0.5562 (mttt) cc_final: 0.4428 (ptpt) REVERT: A 387 ILE cc_start: 0.5463 (OUTLIER) cc_final: 0.5173 (tp) REVERT: A 408 ILE cc_start: 0.7014 (mt) cc_final: 0.6679 (mm) outliers start: 22 outliers final: 12 residues processed: 61 average time/residue: 0.0483 time to fit residues: 3.8746 Evaluate side-chains 59 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.118 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 345 VAL Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 387 ILE Chi-restraints excluded: chain A residue 407 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 0.7980 chunk 21 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 32 optimal weight: 0.5980 chunk 35 optimal weight: 0.0570 chunk 10 optimal weight: 0.7980 chunk 15 optimal weight: 0.7980 chunk 18 optimal weight: 0.6980 chunk 13 optimal weight: 0.1980 overall best weight: 0.3298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4494 r_free = 0.4494 target = 0.197428 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.178836 restraints weight = 4859.048| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4335 r_free = 0.4335 target = 0.181378 restraints weight = 3537.344| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4354 r_free = 0.4354 target = 0.183133 restraints weight = 2754.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4371 r_free = 0.4371 target = 0.184741 restraints weight = 2277.725| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.186025 restraints weight = 1930.234| |-----------------------------------------------------------------------------| r_work (final): 0.4376 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5654 moved from start: 0.4509 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 3049 Z= 0.167 Angle : 0.624 11.172 4143 Z= 0.321 Chirality : 0.041 0.172 490 Planarity : 0.004 0.048 497 Dihedral : 5.868 41.435 407 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.57 % Allowed : 15.24 % Favored : 80.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.23 (0.44), residues: 367 helix: 1.45 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -1.61 (0.66), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 319 TYR 0.007 0.001 TYR A 274 PHE 0.021 0.001 PHE A 257 TRP 0.007 0.001 TRP A 356 HIS 0.006 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00351 / 0.17 ( 3048) covalent geometry : angle 0.62271 / 0.32 ( 4141) SS BOND : bond 0.00884 / 0.47 ( 1) SS BOND : angle 1.67413 / 0.91 ( 2) hydrogen bonds : bond 0.06458 / 4.45 ( 212) hydrogen bonds : angle 4.20545 / 3.11 ( 633) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 42 time to evaluate : 0.108 Fit side-chains REVERT: A 104 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.4171 (m-80) REVERT: A 265 TRP cc_start: 0.7358 (OUTLIER) cc_final: 0.6954 (m-10) REVERT: A 298 HIS cc_start: 0.2519 (OUTLIER) cc_final: 0.1770 (p90) REVERT: A 387 ILE cc_start: 0.5648 (OUTLIER) cc_final: 0.5433 (tp) REVERT: A 408 ILE cc_start: 0.7068 (mt) cc_final: 0.6746 (mm) outliers start: 15 outliers final: 8 residues processed: 51 average time/residue: 0.0501 time to fit residues: 3.4245 Evaluate side-chains 53 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 41 time to evaluate : 0.070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.7980 chunk 9 optimal weight: 0.2980 chunk 17 optimal weight: 0.8980 chunk 31 optimal weight: 0.0870 chunk 21 optimal weight: 0.5980 chunk 13 optimal weight: 0.4980 chunk 14 optimal weight: 0.8980 chunk 36 optimal weight: 0.0970 chunk 2 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 0.3156 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.198214 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4319 r_free = 0.4319 target = 0.179669 restraints weight = 4921.264| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.182150 restraints weight = 3573.262| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4370 r_free = 0.4370 target = 0.184319 restraints weight = 2773.440| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 31)----------------| | r_work = 0.4383 r_free = 0.4383 target = 0.185697 restraints weight = 2244.625| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.4398 r_free = 0.4398 target = 0.187017 restraints weight = 1910.637| |-----------------------------------------------------------------------------| r_work (final): 0.4391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5647 moved from start: 0.4757 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3049 Z= 0.161 Angle : 0.633 13.102 4143 Z= 0.322 Chirality : 0.041 0.167 490 Planarity : 0.004 0.046 497 Dihedral : 5.775 41.181 407 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.88 % Allowed : 15.55 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.24 (0.44), residues: 367 helix: 1.46 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -1.59 (0.66), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 291 TYR 0.007 0.001 TYR A 274 PHE 0.020 0.001 PHE A 257 TRP 0.007 0.001 TRP A 325 HIS 0.006 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00334 / 0.16 ( 3048) covalent geometry : angle 0.63204 / 0.32 ( 4141) SS BOND : bond 0.00645 / 0.34 ( 1) SS BOND : angle 1.42500 / 0.77 ( 2) hydrogen bonds : bond 0.06274 / 4.31 ( 212) hydrogen bonds : angle 4.17670 / 3.09 ( 633) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 43 time to evaluate : 0.072 Fit side-chains REVERT: A 104 PHE cc_start: 0.5857 (OUTLIER) cc_final: 0.4180 (m-80) REVERT: A 265 TRP cc_start: 0.7349 (OUTLIER) cc_final: 0.6980 (m-10) REVERT: A 298 HIS cc_start: 0.2479 (OUTLIER) cc_final: 0.1722 (p90) REVERT: A 387 ILE cc_start: 0.5717 (OUTLIER) cc_final: 0.5489 (tp) REVERT: A 408 ILE cc_start: 0.7105 (mt) cc_final: 0.6793 (mm) outliers start: 16 outliers final: 9 residues processed: 53 average time/residue: 0.0443 time to fit residues: 3.1595 Evaluate side-chains 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 42 time to evaluate : 0.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 89 MET Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 387 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.0670 chunk 25 optimal weight: 0.0370 chunk 11 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 29 optimal weight: 0.0020 chunk 17 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 12 optimal weight: 0.7980 chunk 33 optimal weight: 0.0770 chunk 10 optimal weight: 0.5980 overall best weight: 0.1562 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4542 r_free = 0.4542 target = 0.201779 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4359 r_free = 0.4359 target = 0.183532 restraints weight = 4948.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4389 r_free = 0.4389 target = 0.186217 restraints weight = 3587.478| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4407 r_free = 0.4407 target = 0.188028 restraints weight = 2779.773| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.189753 restraints weight = 2283.667| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4436 r_free = 0.4436 target = 0.190795 restraints weight = 1915.668| |-----------------------------------------------------------------------------| r_work (final): 0.4428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5569 moved from start: 0.4897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3049 Z= 0.136 Angle : 0.654 15.348 4143 Z= 0.313 Chirality : 0.039 0.129 490 Planarity : 0.004 0.046 497 Dihedral : 5.283 40.798 407 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 6.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 3.35 % Allowed : 17.07 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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 (0.44), residues: 367 helix: 1.65 (0.30), residues: 289 sheet: None (None), residues: 0 loop : -1.34 (0.67), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 291 TYR 0.007 0.001 TYR A 119 PHE 0.017 0.001 PHE A 286 TRP 0.007 0.001 TRP A 251 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.14 ( 3048) covalent geometry : angle 0.65402 / 0.31 ( 4141) SS BOND : bond 0.00546 / 0.29 ( 1) SS BOND : angle 1.20723 / 0.65 ( 2) hydrogen bonds : bond 0.05183 / 3.55 ( 212) hydrogen bonds : angle 3.99158 / 2.95 ( 633) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 44 time to evaluate : 0.105 Fit side-chains REVERT: A 104 PHE cc_start: 0.5754 (OUTLIER) cc_final: 0.5526 (m-80) REVERT: A 265 TRP cc_start: 0.7212 (OUTLIER) cc_final: 0.6893 (m-10) REVERT: A 298 HIS cc_start: 0.2387 (OUTLIER) cc_final: 0.1794 (p90) REVERT: A 326 PHE cc_start: 0.6799 (OUTLIER) cc_final: 0.5288 (m-10) REVERT: A 349 MET cc_start: 0.7419 (ppp) cc_final: 0.6854 (ppp) REVERT: A 408 ILE cc_start: 0.7105 (mt) cc_final: 0.6795 (mm) outliers start: 11 outliers final: 5 residues processed: 51 average time/residue: 0.0417 time to fit residues: 2.8676 Evaluate side-chains 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 384 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 35 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 28 optimal weight: 0.0170 chunk 34 optimal weight: 0.1980 chunk 14 optimal weight: 0.8980 chunk 33 optimal weight: 0.1980 chunk 19 optimal weight: 0.8980 chunk 31 optimal weight: 0.2980 chunk 12 optimal weight: 0.6980 overall best weight: 0.2818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 35 HIS ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.200239 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.182077 restraints weight = 4830.978| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.184742 restraints weight = 3492.720| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.186585 restraints weight = 2684.521| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4404 r_free = 0.4404 target = 0.188275 restraints weight = 2207.556| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.4414 r_free = 0.4414 target = 0.189302 restraints weight = 1852.689| |-----------------------------------------------------------------------------| r_work (final): 0.4411 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5609 moved from start: 0.4979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3049 Z= 0.155 Angle : 0.682 15.089 4143 Z= 0.332 Chirality : 0.040 0.128 490 Planarity : 0.005 0.047 497 Dihedral : 5.326 39.839 407 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 7.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 2.44 % Allowed : 18.29 % Favored : 79.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.47 (0.44), residues: 367 helix: 1.59 (0.30), residues: 289 sheet: None (None), residues: 0 loop : -1.33 (0.68), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.007 0.001 TYR A 274 PHE 0.019 0.001 PHE A 257 TRP 0.006 0.001 TRP A 325 HIS 0.007 0.002 HIS A 35 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.15 ( 3048) covalent geometry : angle 0.68151 / 0.33 ( 4141) SS BOND : bond 0.00642 / 0.34 ( 1) SS BOND : angle 1.43352 / 0.78 ( 2) hydrogen bonds : bond 0.05745 / 3.92 ( 212) hydrogen bonds : angle 4.03643 / 2.98 ( 633) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 734 Ramachandran restraints generated. 367 Oldfield, 0 Emsley, 367 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.112 Fit side-chains REVERT: A 104 PHE cc_start: 0.5776 (OUTLIER) cc_final: 0.5529 (m-80) REVERT: A 298 HIS cc_start: 0.2392 (OUTLIER) cc_final: 0.1799 (p90) REVERT: A 408 ILE cc_start: 0.7158 (mt) cc_final: 0.6865 (mm) outliers start: 8 outliers final: 6 residues processed: 44 average time/residue: 0.0452 time to fit residues: 2.7144 Evaluate side-chains 45 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 37 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 ILE Chi-restraints excluded: chain A residue 53 TRP Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 7 optimal weight: 0.8980 chunk 32 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 28 optimal weight: 0.0070 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.1980 chunk 4 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.0470 chunk 17 optimal weight: 1.9990 chunk 9 optimal weight: 0.2980 overall best weight: 0.1296 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 135 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4551 r_free = 0.4551 target = 0.203670 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.185824 restraints weight = 4821.842| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4402 r_free = 0.4402 target = 0.188346 restraints weight = 3480.338| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.4428 r_free = 0.4428 target = 0.190714 restraints weight = 2698.081| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4444 r_free = 0.4444 target = 0.192385 restraints weight = 2156.009| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.4453 r_free = 0.4453 target = 0.193273 restraints weight = 1784.797| |-----------------------------------------------------------------------------| r_work (final): 0.4445 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5513 moved from start: 0.5117 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3049 Z= 0.131 Angle : 0.654 15.626 4143 Z= 0.309 Chirality : 0.039 0.128 490 Planarity : 0.004 0.046 497 Dihedral : 4.587 18.033 405 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.74 % Allowed : 18.29 % Favored : 78.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 9.09 % 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: 1.75 (0.44), residues: 367 helix: 1.76 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -1.14 (0.71), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.000 0.000 ARG A 291 TYR 0.007 0.001 TYR A 119 PHE 0.015 0.001 PHE A 286 TRP 0.008 0.001 TRP A 251 HIS 0.003 0.001 HIS A 108 Details of bonding type rmsd/Z covalent geometry : bond 0.00257 / 0.13 ( 3048) covalent geometry : angle 0.65339 / 0.31 ( 4141) SS BOND : bond 0.00469 / 0.25 ( 1) SS BOND : angle 1.00740 / 0.55 ( 2) hydrogen bonds : bond 0.04767 / 3.24 ( 212) hydrogen bonds : angle 3.90547 / 2.88 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 741.36 seconds wall clock time: 13 minutes 29.32 seconds (809.32 seconds total)