Starting phenix.real_space_refine on Tue Aug 4 12:47:52 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9k7s_62152/08_2026/9k7s_62152.cif Found real_map, /net/cci-nas-00/data/ceres_data/9k7s_62152/08_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/9k7s_62152/08_2026/9k7s_62152.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9k7s_62152/08_2026/9k7s_62152.map" model { file = "/net/cci-nas-00/data/ceres_data/9k7s_62152/08_2026/9k7s_62152.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9k7s_62152/08_2026/9k7s_62152.cif" } 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-2.2rc3-6140/lib/python3.11/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: 1.12, per 1000 atoms: 0.38 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: 0.32 Conformation dependent library (CDL) restraints added in 140.7 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: 0.04 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: 0.47 Time building geometry restraints manager: 0.41 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=" 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 bond pdb=" CA ILE A 85 " pdb=" C ILE A 85 " ideal model delta sigma weight residual 1.526 1.534 -0.007 7.90e-03 1.60e+04 8.78e-01 bond pdb=" CA CYS A 143 " pdb=" CB CYS A 143 " ideal model delta sigma weight residual 1.529 1.545 -0.016 1.74e-02 3.30e+03 8.63e-01 bond pdb=" N THR A 383 " pdb=" CA THR A 383 " ideal model delta sigma weight residual 1.459 1.469 -0.010 1.21e-02 6.83e+03 6.93e-01 bond pdb=" N CYS A 143 " pdb=" CA CYS A 143 " ideal model delta sigma weight residual 1.458 1.468 -0.011 1.33e-02 5.65e+03 6.57e-01 ... (remaining 3043 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.36: 4054 1.36 - 2.73: 69 2.73 - 4.09: 9 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: 262 0.025 - 0.050: 130 0.050 - 0.075: 71 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: 0.610 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: 0.070 Check model and map are aligned: 0.010 Set scattering table: 0.010 Process input model: 4.990 Find NCS groups from input model: 0.010 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:1.160 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 6.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5403 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= 0.146 Angle : 0.507 6.819 4143 Z= 0.282 Chirality : 0.039 0.126 490 Planarity : 0.004 0.039 497 Dihedral : 11.736 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 0.00255 / 0.15 ( 3048) covalent geometry : angle 0.50583 / 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 : 0.104 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: 0.0459 time to fit residues: 3.6863 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 : 0.102 ------------------------------------------------------------------------------- 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: 0.6980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 105 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4566 r_free = 0.4566 target = 0.203907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.182410 restraints weight = 5016.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4390 r_free = 0.4390 target = 0.186040 restraints weight = 3394.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4418 r_free = 0.4418 target = 0.188718 restraints weight = 2509.242| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 27)----------------| | r_work = 0.4434 r_free = 0.4434 target = 0.190380 restraints weight = 1982.886| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4450 r_free = 0.4450 target = 0.191927 restraints weight = 1666.785| |-----------------------------------------------------------------------------| r_work (final): 0.4436 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5694 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3049 Z= 0.189 Angle : 0.614 6.749 4143 Z= 0.330 Chirality : 0.041 0.143 490 Planarity : 0.004 0.045 497 Dihedral : 6.921 48.043 407 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 5.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.09 % Favored : 98.91 % Rotamer: Outliers : 4.88 % Allowed : 7.01 % 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: 2.56 (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 307 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 0.00384 / 0.19 ( 3048) covalent geometry : angle 0.61043 / 0.33 ( 4141) SS BOND : bond 0.01476 / 0.78 ( 1) SS BOND : angle 2.92127 / 1.60 ( 2) hydrogen bonds : bond 0.07054 / 4.85 ( 212) hydrogen bonds : angle 4.19268 / 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 69 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 53 time to evaluate : 0.105 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 169 LEU cc_start: 0.3517 (OUTLIER) cc_final: 0.3125 (tt) REVERT: A 247 PHE cc_start: 0.6215 (t80) cc_final: 0.5975 (t80) REVERT: A 265 TRP cc_start: 0.7141 (OUTLIER) cc_final: 0.6811 (m-10) REVERT: A 298 HIS cc_start: 0.2741 (OUTLIER) cc_final: 0.2111 (p90) REVERT: A 347 MET cc_start: 0.6591 (mmt) cc_final: 0.6069 (mmp) REVERT: A 374 LYS cc_start: 0.5024 (mttt) cc_final: 0.4477 (tptp) REVERT: A 408 ILE cc_start: 0.7045 (mt) cc_final: 0.6768 (mm) outliers start: 16 outliers final: 7 residues processed: 64 average time/residue: 0.0522 time to fit residues: 4.2824 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 : 0.103 ------------------------------------------------------------------------------- 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: 0.1980 chunk 0 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 12 optimal weight: 0.5980 chunk 20 optimal weight: 0.2980 chunk 31 optimal weight: 0.0970 overall best weight: 0.3378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4556 r_free = 0.4556 target = 0.202404 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.179897 restraints weight = 5132.190| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.183491 restraints weight = 3527.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.4391 r_free = 0.4391 target = 0.186019 restraints weight = 2642.805| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4413 r_free = 0.4413 target = 0.188082 restraints weight = 2139.812| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.189425 restraints weight = 1780.769| |-----------------------------------------------------------------------------| r_work (final): 0.4413 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5723 moved from start: 0.2711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3049 Z= 0.165 Angle : 0.586 8.243 4143 Z= 0.309 Chirality : 0.040 0.164 490 Planarity : 0.004 0.045 497 Dihedral : 6.628 48.484 407 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 4.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 5.18 % Allowed : 10.06 % Favored : 84.76 % 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: 2.43 (0.44), residues: 367 helix: 2.22 (0.30), residues: 281 sheet: None (None), residues: 0 loop : -0.46 (0.70), residues: 86 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.009 0.001 TYR A 274 PHE 0.018 0.001 PHE A 42 TRP 0.007 0.001 TRP A 53 HIS 0.005 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00335 / 0.17 ( 3048) covalent geometry : angle 0.58470 / 0.31 ( 4141) SS BOND : bond 0.00933 / 0.49 ( 1) SS BOND : angle 1.94558 / 1.05 ( 2) hydrogen bonds : bond 0.06450 / 4.43 ( 212) hydrogen bonds : angle 4.02454 / 2.94 ( 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 65 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 48 time to evaluate : 0.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 298 HIS cc_start: 0.2716 (OUTLIER) cc_final: 0.2099 (p90) REVERT: A 347 MET cc_start: 0.6322 (mmt) cc_final: 0.5934 (mmp) REVERT: A 374 LYS cc_start: 0.4979 (mttt) cc_final: 0.4498 (tptp) REVERT: A 408 ILE cc_start: 0.7015 (mt) cc_final: 0.6749 (mm) outliers start: 17 outliers final: 9 residues processed: 58 average time/residue: 0.0512 time to fit residues: 3.7413 Evaluate side-chains 55 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 45 time to evaluate : 0.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS 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: 0.3980 chunk 36 optimal weight: 0.3980 chunk 24 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 16 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 0.5980 chunk 30 optimal weight: 0.5980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4506 r_free = 0.4506 target = 0.197927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.177297 restraints weight = 5011.586| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4320 r_free = 0.4320 target = 0.180229 restraints weight = 3585.090| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.182540 restraints weight = 2754.696| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 38)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.184300 restraints weight = 2226.122| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.185460 restraints weight = 1876.591| |-----------------------------------------------------------------------------| r_work (final): 0.4381 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5840 moved from start: 0.3553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3049 Z= 0.210 Angle : 0.637 8.818 4143 Z= 0.339 Chirality : 0.042 0.131 490 Planarity : 0.004 0.044 497 Dihedral : 6.693 47.200 407 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 4.57 % Allowed : 13.72 % Favored : 81.71 % 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: 1.53 (0.44), residues: 367 helix: 1.67 (0.31), residues: 287 sheet: None (None), residues: 0 loop : -1.39 (0.67), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.013 0.001 TYR A 274 PHE 0.016 0.002 PHE A 307 TRP 0.010 0.002 TRP A 53 HIS 0.007 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00446 / 0.21 ( 3048) covalent geometry : angle 0.63601 / 0.34 ( 4141) SS BOND : bond 0.01067 / 0.56 ( 1) SS BOND : angle 1.98555 / 1.07 ( 2) hydrogen bonds : bond 0.07513 / 5.18 ( 212) hydrogen bonds : angle 4.30166 / 3.17 ( 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 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 46 time to evaluate : 0.109 Fit side-chains REVERT: A 153 MET cc_start: 0.5005 (tpp) cc_final: 0.4793 (tpp) REVERT: A 187 LYS cc_start: 0.6287 (mttt) cc_final: 0.6007 (mttt) REVERT: A 265 TRP cc_start: 0.7432 (OUTLIER) cc_final: 0.7108 (m-10) REVERT: A 298 HIS cc_start: 0.2672 (OUTLIER) cc_final: 0.1983 (p90) REVERT: A 335 PRO cc_start: 0.3216 (Cg_endo) cc_final: 0.2821 (Cg_exo) REVERT: A 347 MET cc_start: 0.6128 (mmt) cc_final: 0.5680 (mmp) REVERT: A 374 LYS cc_start: 0.5456 (mttt) cc_final: 0.5160 (tptp) REVERT: A 408 ILE cc_start: 0.7060 (mt) cc_final: 0.6724 (mm) outliers start: 15 outliers final: 11 residues processed: 56 average time/residue: 0.0565 time to fit residues: 4.0230 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 : 0.109 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS Chi-restraints excluded: chain A residue 73 LEU 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 332 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: 0.0050 chunk 33 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.4980 chunk 26 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 17 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 16 optimal weight: 0.6980 overall best weight: 0.3994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4505 r_free = 0.4505 target = 0.198748 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.178353 restraints weight = 4887.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.4330 r_free = 0.4330 target = 0.181353 restraints weight = 3412.033| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.183335 restraints weight = 2585.864| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 39)----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.185257 restraints weight = 2118.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 32)----------------| | r_work = 0.4386 r_free = 0.4386 target = 0.186595 restraints weight = 1771.057| |-----------------------------------------------------------------------------| r_work (final): 0.4378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5803 moved from start: 0.3850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3049 Z= 0.175 Angle : 0.607 10.046 4143 Z= 0.319 Chirality : 0.041 0.131 490 Planarity : 0.004 0.043 497 Dihedral : 6.438 45.601 407 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 5.18 % Allowed : 13.72 % 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: 1.44 (0.45), residues: 367 helix: 1.61 (0.31), residues: 287 sheet: None (None), residues: 0 loop : -1.44 (0.68), residues: 80 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 319 TYR 0.009 0.001 TYR A 274 PHE 0.024 0.001 PHE A 257 TRP 0.006 0.001 TRP A 53 HIS 0.007 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00365 / 0.18 ( 3048) covalent geometry : angle 0.60554 / 0.32 ( 4141) SS BOND : bond 0.00751 / 0.40 ( 1) SS BOND : angle 1.72561 / 0.92 ( 2) hydrogen bonds : bond 0.06794 / 4.66 ( 212) hydrogen bonds : angle 4.15555 / 3.07 ( 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: 17 poor density : 46 time to evaluate : 0.105 Fit side-chains REVERT: A 104 PHE cc_start: 0.5775 (OUTLIER) cc_final: 0.4401 (m-80) REVERT: A 187 LYS cc_start: 0.6059 (mttt) cc_final: 0.5837 (mttt) REVERT: A 265 TRP cc_start: 0.7393 (OUTLIER) cc_final: 0.7066 (m-10) REVERT: A 298 HIS cc_start: 0.2677 (OUTLIER) cc_final: 0.1959 (p90) REVERT: A 335 PRO cc_start: 0.3431 (Cg_endo) cc_final: 0.3165 (Cg_exo) REVERT: A 374 LYS cc_start: 0.5810 (mttt) cc_final: 0.5024 (tptp) REVERT: A 386 VAL cc_start: 0.4772 (OUTLIER) cc_final: 0.4009 (m) REVERT: A 408 ILE cc_start: 0.7084 (mt) cc_final: 0.6773 (mm) outliers start: 17 outliers final: 11 residues processed: 56 average time/residue: 0.0567 time to fit residues: 4.0259 Evaluate side-chains 59 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 44 time to evaluate : 0.103 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS 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 326 PHE Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 PHE Chi-restraints excluded: chain A residue 386 VAL 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: 0.0970 chunk 12 optimal weight: 0.5980 chunk 14 optimal weight: 0.9990 chunk 4 optimal weight: 0.9980 chunk 19 optimal weight: 0.0010 chunk 8 optimal weight: 0.6980 chunk 3 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 18 optimal weight: 0.7980 chunk 33 optimal weight: 0.6980 overall best weight: 0.3984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4498 r_free = 0.4498 target = 0.198316 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.4293 r_free = 0.4293 target = 0.177920 restraints weight = 4898.080| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.4322 r_free = 0.4322 target = 0.180784 restraints weight = 3386.397| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4349 r_free = 0.4349 target = 0.183210 restraints weight = 2572.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.4365 r_free = 0.4365 target = 0.184809 restraints weight = 2064.257| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.186325 restraints weight = 1746.230| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5812 moved from start: 0.4191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 3049 Z= 0.176 Angle : 0.606 9.273 4143 Z= 0.317 Chirality : 0.041 0.180 490 Planarity : 0.004 0.042 497 Dihedral : 6.308 43.631 407 Min Nonbonded Distance : 2.511 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 5.49 % Allowed : 14.02 % 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: 1.23 (0.44), residues: 367 helix: 1.46 (0.30), residues: 291 sheet: None (None), residues: 0 loop : -1.67 (0.66), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.009 0.001 TYR A 274 PHE 0.020 0.001 PHE A 257 TRP 0.006 0.001 TRP A 325 HIS 0.006 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00374 / 0.18 ( 3048) covalent geometry : angle 0.60535 / 0.32 ( 4141) SS BOND : bond 0.00811 / 0.43 ( 1) SS BOND : angle 1.68039 / 0.91 ( 2) hydrogen bonds : bond 0.06708 / 4.61 ( 212) hydrogen bonds : angle 4.19709 / 3.10 ( 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 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 43 time to evaluate : 0.102 Fit side-chains revert: symmetry clash REVERT: A 104 PHE cc_start: 0.5780 (OUTLIER) cc_final: 0.4260 (m-80) REVERT: A 265 TRP cc_start: 0.7321 (OUTLIER) cc_final: 0.6946 (m-10) REVERT: A 298 HIS cc_start: 0.2668 (OUTLIER) cc_final: 0.1953 (p90) REVERT: A 374 LYS cc_start: 0.5558 (mttt) cc_final: 0.5129 (tptp) REVERT: A 408 ILE cc_start: 0.7071 (mt) cc_final: 0.6726 (mm) outliers start: 18 outliers final: 10 residues processed: 56 average time/residue: 0.0481 time to fit residues: 3.5081 Evaluate side-chains 56 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 43 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 23 optimal weight: 0.1980 chunk 21 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 2 optimal weight: 0.3980 chunk 24 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 10 optimal weight: 0.5980 chunk 15 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4501 r_free = 0.4501 target = 0.197025 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.4278 r_free = 0.4278 target = 0.175968 restraints weight = 4969.577| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.179099 restraints weight = 3408.467| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.181657 restraints weight = 2547.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.4366 r_free = 0.4366 target = 0.183625 restraints weight = 2013.535| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4380 r_free = 0.4380 target = 0.184907 restraints weight = 1650.771| |-----------------------------------------------------------------------------| r_work (final): 0.4372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5863 moved from start: 0.4599 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3049 Z= 0.200 Angle : 0.655 11.149 4143 Z= 0.341 Chirality : 0.042 0.125 490 Planarity : 0.005 0.049 497 Dihedral : 6.374 42.652 407 Min Nonbonded Distance : 2.503 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 4.88 % Allowed : 16.16 % 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: 0.94 (0.43), residues: 367 helix: 1.28 (0.30), residues: 291 sheet: None (None), residues: 0 loop : -1.86 (0.63), residues: 76 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.010 0.001 TYR A 274 PHE 0.020 0.002 PHE A 257 TRP 0.007 0.001 TRP A 325 HIS 0.008 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00428 / 0.20 ( 3048) covalent geometry : angle 0.65385 / 0.34 ( 4141) SS BOND : bond 0.00868 / 0.46 ( 1) SS BOND : angle 1.90959 / 1.04 ( 2) hydrogen bonds : bond 0.07307 / 5.00 ( 212) hydrogen bonds : angle 4.40658 / 3.28 ( 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 64 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 48 time to evaluate : 0.158 Fit side-chains REVERT: A 104 PHE cc_start: 0.5816 (OUTLIER) cc_final: 0.4287 (m-80) REVERT: A 265 TRP cc_start: 0.7283 (OUTLIER) cc_final: 0.6796 (m-10) REVERT: A 298 HIS cc_start: 0.2675 (OUTLIER) cc_final: 0.1953 (p90) REVERT: A 374 LYS cc_start: 0.5541 (mttt) cc_final: 0.5142 (tptp) REVERT: A 408 ILE cc_start: 0.7096 (mt) cc_final: 0.6738 (mm) outliers start: 16 outliers final: 10 residues processed: 59 average time/residue: 0.0527 time to fit residues: 4.0472 Evaluate side-chains 58 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 45 time to evaluate : 0.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 35 HIS 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 326 PHE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 19 optimal weight: 0.9990 chunk 9 optimal weight: 0.3980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.0870 chunk 21 optimal weight: 0.7980 chunk 13 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 36 optimal weight: 0.2980 chunk 2 optimal weight: 0.4980 chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 0.1980 overall best weight: 0.2758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4520 r_free = 0.4520 target = 0.199372 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4296 r_free = 0.4296 target = 0.177916 restraints weight = 5033.668| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4334 r_free = 0.4334 target = 0.181295 restraints weight = 3434.980| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4357 r_free = 0.4357 target = 0.183579 restraints weight = 2556.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 36)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.185700 restraints weight = 2042.379| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 18)----------------| | r_work = 0.4395 r_free = 0.4395 target = 0.187000 restraints weight = 1684.914| |-----------------------------------------------------------------------------| r_work (final): 0.4392 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5808 moved from start: 0.4669 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= 0.157 Angle : 0.633 12.795 4143 Z= 0.319 Chirality : 0.041 0.178 490 Planarity : 0.004 0.046 497 Dihedral : 5.974 41.107 407 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 5.49 % Allowed : 17.07 % Favored : 77.44 % 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: 1.25 (0.44), residues: 367 helix: 1.49 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -1.68 (0.65), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 291 TYR 0.007 0.001 TYR A 274 PHE 0.018 0.001 PHE A 247 TRP 0.005 0.001 TRP A 53 HIS 0.005 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00324 / 0.16 ( 3048) covalent geometry : angle 0.63242 / 0.32 ( 4141) SS BOND : bond 0.00703 / 0.37 ( 1) SS BOND : angle 1.48596 / 0.80 ( 2) hydrogen bonds : bond 0.06130 / 4.19 ( 212) hydrogen bonds : angle 4.18351 / 3.10 ( 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 63 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 45 time to evaluate : 0.103 Fit side-chains REVERT: A 104 PHE cc_start: 0.5670 (OUTLIER) cc_final: 0.4048 (m-80) REVERT: A 298 HIS cc_start: 0.2664 (OUTLIER) cc_final: 0.1979 (p90) REVERT: A 374 LYS cc_start: 0.5427 (mttt) cc_final: 0.5120 (tptp) REVERT: A 408 ILE cc_start: 0.7061 (mt) cc_final: 0.6700 (mm) outliers start: 18 outliers final: 14 residues processed: 56 average time/residue: 0.0435 time to fit residues: 3.2761 Evaluate side-chains 61 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 45 time to evaluate : 0.102 ------------------------------------------------------------------------------- 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 205 PHE Chi-restraints excluded: chain A residue 265 TRP Chi-restraints excluded: chain A residue 268 SER Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 298 HIS Chi-restraints excluded: chain A residue 326 PHE Chi-restraints excluded: chain A residue 349 MET Chi-restraints excluded: chain A residue 360 VAL Chi-restraints excluded: chain A residue 384 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.2980 chunk 25 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 0.6980 chunk 29 optimal weight: 0.1980 chunk 17 optimal weight: 0.5980 chunk 15 optimal weight: 0.1980 chunk 24 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 33 optimal weight: 0.0370 chunk 10 optimal weight: 0.3980 overall best weight: 0.1858 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4538 r_free = 0.4538 target = 0.201556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.183013 restraints weight = 4983.456| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 23)----------------| | r_work = 0.4381 r_free = 0.4381 target = 0.185877 restraints weight = 3521.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.4405 r_free = 0.4405 target = 0.188106 restraints weight = 2670.809| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.4421 r_free = 0.4421 target = 0.189656 restraints weight = 2125.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4435 r_free = 0.4435 target = 0.191014 restraints weight = 1790.917| |-----------------------------------------------------------------------------| r_work (final): 0.4425 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5710 moved from start: 0.4804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3049 Z= 0.140 Angle : 0.641 15.045 4143 Z= 0.313 Chirality : 0.039 0.156 490 Planarity : 0.004 0.045 497 Dihedral : 5.593 39.117 407 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 5.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.96 % Allowed : 18.90 % Favored : 77.13 % 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: 1.37 (0.44), residues: 367 helix: 1.52 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -1.42 (0.67), residues: 77 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 0.016 0.001 PHE A 247 TRP 0.005 0.001 TRP A 251 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00278 / 0.14 ( 3048) covalent geometry : angle 0.64054 / 0.31 ( 4141) SS BOND : bond 0.00587 / 0.31 ( 1) SS BOND : angle 1.31915 / 0.72 ( 2) hydrogen bonds : bond 0.05433 / 3.71 ( 212) hydrogen bonds : angle 4.03026 / 2.99 ( 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: 13 poor density : 42 time to evaluate : 0.127 Fit side-chains REVERT: A 104 PHE cc_start: 0.5725 (OUTLIER) cc_final: 0.4168 (m-80) REVERT: A 298 HIS cc_start: 0.2481 (OUTLIER) cc_final: 0.1760 (p90) REVERT: A 374 LYS cc_start: 0.5799 (mttt) cc_final: 0.5304 (ttmm) REVERT: A 408 ILE cc_start: 0.7111 (mt) cc_final: 0.6809 (mm) outliers start: 13 outliers final: 8 residues processed: 50 average time/residue: 0.0578 time to fit residues: 3.7695 Evaluate side-chains 49 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 39 time to evaluate : 0.107 ------------------------------------------------------------------------------- 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 89 MET 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 326 PHE Chi-restraints excluded: chain A residue 349 MET 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: 0.6980 chunk 0 optimal weight: 2.9990 chunk 26 optimal weight: 0.9980 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.1980 chunk 34 optimal weight: 0.5980 chunk 14 optimal weight: 0.3980 chunk 33 optimal weight: 0.2980 chunk 19 optimal weight: 0.2980 chunk 31 optimal weight: 0.0870 chunk 12 optimal weight: 0.0980 overall best weight: 0.1958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 35 HIS ** A 284 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 = 0.4539 r_free = 0.4539 target = 0.201679 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.4326 r_free = 0.4326 target = 0.180638 restraints weight = 4874.795| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.4364 r_free = 0.4364 target = 0.184165 restraints weight = 3278.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.4392 r_free = 0.4392 target = 0.186801 restraints weight = 2400.769| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.4411 r_free = 0.4411 target = 0.188668 restraints weight = 1875.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.4426 r_free = 0.4426 target = 0.190079 restraints weight = 1539.921| |-----------------------------------------------------------------------------| r_work (final): 0.4416 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5727 moved from start: 0.4940 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= 0.142 Angle : 0.649 15.135 4143 Z= 0.318 Chirality : 0.040 0.149 490 Planarity : 0.004 0.046 497 Dihedral : 5.059 28.208 405 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 3.35 % Allowed : 19.21 % Favored : 77.44 % 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: 1.46 (0.44), residues: 367 helix: 1.55 (0.30), residues: 289 sheet: None (None), residues: 0 loop : -1.18 (0.70), residues: 78 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 291 TYR 0.007 0.001 TYR A 119 PHE 0.020 0.001 PHE A 42 TRP 0.004 0.001 TRP A 356 HIS 0.003 0.001 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00282 / 0.14 ( 3048) covalent geometry : angle 0.64878 / 0.32 ( 4141) SS BOND : bond 0.00631 / 0.33 ( 1) SS BOND : angle 1.37585 / 0.75 ( 2) hydrogen bonds : bond 0.05423 / 3.67 ( 212) hydrogen bonds : angle 3.97894 / 2.94 ( 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 51 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 40 time to evaluate : 0.109 Fit side-chains REVERT: A 104 PHE cc_start: 0.5621 (OUTLIER) cc_final: 0.4027 (m-80) REVERT: A 298 HIS cc_start: 0.2554 (OUTLIER) cc_final: 0.2019 (p90) REVERT: A 408 ILE cc_start: 0.7120 (mt) cc_final: 0.6818 (mm) outliers start: 11 outliers final: 8 residues processed: 48 average time/residue: 0.0466 time to fit residues: 2.9741 Evaluate side-chains 47 residues out of total 332 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 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 89 MET 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 326 PHE Chi-restraints excluded: chain A residue 349 MET 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: 0.5980 chunk 32 optimal weight: 0.9990 chunk 13 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 1 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 5 optimal weight: 0.0470 chunk 17 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.4878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** 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 = 0.4503 r_free = 0.4503 target = 0.197924 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.179603 restraints weight = 4812.841| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.182280 restraints weight = 3399.702| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.4367 r_free = 0.4367 target = 0.184289 restraints weight = 2588.317| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.185957 restraints weight = 2089.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.4394 r_free = 0.4394 target = 0.186766 restraints weight = 1746.916| |-----------------------------------------------------------------------------| r_work (final): 0.4387 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5813 moved from start: 0.5118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3049 Z= 0.193 Angle : 0.707 14.887 4143 Z= 0.353 Chirality : 0.042 0.142 490 Planarity : 0.005 0.046 497 Dihedral : 5.404 30.458 405 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer: Outliers : 3.05 % Allowed : 19.51 % Favored : 77.44 % 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: 1.17 (0.44), residues: 367 helix: 1.39 (0.30), residues: 290 sheet: None (None), residues: 0 loop : -1.52 (0.68), residues: 77 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.001 ARG A 319 TYR 0.009 0.001 TYR A 274 PHE 0.028 0.002 PHE A 42 TRP 0.007 0.001 TRP A 325 HIS 0.007 0.002 HIS A 262 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.19 ( 3048) covalent geometry : angle 0.70555 / 0.35 ( 4141) SS BOND : bond 0.00876 / 0.46 ( 1) SS BOND : angle 1.81770 / 0.99 ( 2) hydrogen bonds : bond 0.06785 / 4.63 ( 212) hydrogen bonds : angle 4.23065 / 3.14 ( 633) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 749.13 seconds wall clock time: 13 minutes 32.29 seconds (812.29 seconds total)