Starting phenix.real_space_refine on Tue Mar 3 12:37:09 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8de9_27388/03_2026/8de9_27388.cif Found real_map, /net/cci-nas-00/data/ceres_data/8de9_27388/03_2026/8de9_27388.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8de9_27388/03_2026/8de9_27388.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8de9_27388/03_2026/8de9_27388.map" model { file = "/net/cci-nas-00/data/ceres_data/8de9_27388/03_2026/8de9_27388.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8de9_27388/03_2026/8de9_27388.cif" } resolution = 3.4 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= 0.002 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: 6 Type Number sf(0) Gaussians K 3 8.98 5 P 1 5.49 5 S 16 5.16 5 C 2760 2.51 5 N 626 2.21 5 O 709 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 4115 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2035 Number of conformers: 1 Conformer: "" Number of residues, atoms: 259, 2035 Classifications: {'peptide': 259} Link IDs: {'PTRANS': 7, 'TRANS': 251} Chain: "B" Number of atoms: 2028 Number of conformers: 1 Conformer: "" Number of residues, atoms: 258, 2028 Classifications: {'peptide': 258} Link IDs: {'PTRANS': 7, 'TRANS': 250} Chain: "A" Number of atoms: 52 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 52 Unusual residues: {' K': 3, 'PEV': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Time building chain proxies: 1.12, per 1000 atoms: 0.27 Number of scatterers: 4115 At special positions: 0 Unit cell: (80.514, 97.128, 79.236, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 3 19.00 S 16 16.00 P 1 15.00 O 709 8.00 N 626 7.00 C 2760 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 93 " - pdb=" SG CYS B 93 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.35 Conformation dependent library (CDL) restraints added in 128.9 milliseconds 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 938 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 0 sheets defined 78.5% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.07 Creating SS restraints... Processing helix chain 'A' and resid 43 through 91 removed outlier: 3.569A pdb=" N ALA A 67 " --> pdb=" O THR A 63 " (cutoff:3.500A) Proline residue: A 71 - end of helix Processing helix chain 'A' and resid 95 through 113 Processing helix chain 'A' and resid 128 through 142 Processing helix chain 'A' and resid 152 through 196 removed outlier: 3.561A pdb=" N ILE A 157 " --> pdb=" O GLU A 153 " (cutoff:3.500A) Proline residue: A 168 - end of helix Processing helix chain 'A' and resid 202 through 234 removed outlier: 3.894A pdb=" N LEU A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Proline residue: A 226 - end of helix Processing helix chain 'A' and resid 237 through 250 Processing helix chain 'A' and resid 269 through 298 removed outlier: 3.702A pdb=" N ILE A 273 " --> pdb=" O TYR A 269 " (cutoff:3.500A) Processing helix chain 'B' and resid 43 through 91 Proline residue: B 71 - end of helix Processing helix chain 'B' and resid 95 through 113 removed outlier: 3.580A pdb=" N ALA B 112 " --> pdb=" O LEU B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 128 through 142 Processing helix chain 'B' and resid 152 through 193 Proline residue: B 168 - end of helix Processing helix chain 'B' and resid 204 through 223 Processing helix chain 'B' and resid 223 through 235 removed outlier: 3.713A pdb=" N ALA B 227 " --> pdb=" O VAL B 223 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU B 228 " --> pdb=" O ALA B 224 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N ILE B 229 " --> pdb=" O LEU B 225 " (cutoff:3.500A) Processing helix chain 'B' and resid 237 through 250 Processing helix chain 'B' and resid 269 through 297 323 hydrogen bonds defined for protein. 969 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.56 Time building geometry restraints manager: 0.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 623 1.31 - 1.44: 1184 1.44 - 1.56: 2381 1.56 - 1.69: 3 1.69 - 1.81: 26 Bond restraints: 4217 Sorted by residual: bond pdb=" CA ILE B 264 " pdb=" C ILE B 264 " ideal model delta sigma weight residual 1.530 1.584 -0.053 1.12e-02 7.97e+03 2.27e+01 bond pdb=" C31 PEV A 401 " pdb=" O2 PEV A 401 " ideal model delta sigma weight residual 1.330 1.409 -0.079 2.00e-02 2.50e+03 1.56e+01 bond pdb=" C11 PEV A 401 " pdb=" O3 PEV A 401 " ideal model delta sigma weight residual 1.335 1.398 -0.063 2.00e-02 2.50e+03 9.77e+00 bond pdb=" CA THR A 251 " pdb=" C THR A 251 " ideal model delta sigma weight residual 1.525 1.488 0.037 1.40e-02 5.10e+03 7.01e+00 bond pdb=" N THR A 251 " pdb=" CA THR A 251 " ideal model delta sigma weight residual 1.461 1.431 0.031 1.49e-02 4.50e+03 4.26e+00 ... (remaining 4212 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.27: 5583 3.27 - 6.55: 121 6.55 - 9.82: 12 9.82 - 13.09: 4 13.09 - 16.36: 1 Bond angle restraints: 5721 Sorted by residual: angle pdb=" C ILE B 264 " pdb=" CA ILE B 264 " pdb=" CB ILE B 264 " ideal model delta sigma weight residual 112.19 102.19 10.00 1.15e+00 7.56e-01 7.56e+01 angle pdb=" N GLU B 263 " pdb=" CA GLU B 263 " pdb=" C GLU B 263 " ideal model delta sigma weight residual 111.17 122.10 -10.93 1.41e+00 5.03e-01 6.01e+01 angle pdb=" C GLU B 263 " pdb=" CA GLU B 263 " pdb=" CB GLU B 263 " ideal model delta sigma weight residual 112.06 101.34 10.72 1.57e+00 4.06e-01 4.66e+01 angle pdb=" N TRP A 199 " pdb=" CA TRP A 199 " pdb=" C TRP A 199 " ideal model delta sigma weight residual 108.52 118.91 -10.39 1.63e+00 3.76e-01 4.06e+01 angle pdb=" O3P PEV A 401 " pdb=" P PEV A 401 " pdb=" O4P PEV A 401 " ideal model delta sigma weight residual 93.57 109.93 -16.36 3.00e+00 1.11e-01 2.98e+01 ... (remaining 5716 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.26: 2302 27.26 - 54.53: 105 54.53 - 81.79: 8 81.79 - 109.05: 0 109.05 - 136.32: 1 Dihedral angle restraints: 2416 sinusoidal: 947 harmonic: 1469 Sorted by residual: dihedral pdb=" CA GLN B 122 " pdb=" C GLN B 122 " pdb=" N GLU B 123 " pdb=" CA GLU B 123 " ideal model delta harmonic sigma weight residual 180.00 150.90 29.10 0 5.00e+00 4.00e-02 3.39e+01 dihedral pdb=" C3 PEV A 401 " pdb=" C1 PEV A 401 " pdb=" C2 PEV A 401 " pdb=" O3P PEV A 401 " ideal model delta sinusoidal sigma weight residual 292.80 156.48 136.32 1 3.00e+01 1.11e-03 1.84e+01 dihedral pdb=" CA LEU B 68 " pdb=" C LEU B 68 " pdb=" N GLU B 69 " pdb=" CA GLU B 69 " ideal model delta harmonic sigma weight residual -180.00 -161.10 -18.90 0 5.00e+00 4.00e-02 1.43e+01 ... (remaining 2413 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 591 0.089 - 0.178: 68 0.178 - 0.266: 5 0.266 - 0.355: 1 0.355 - 0.444: 2 Chirality restraints: 667 Sorted by residual: chirality pdb=" CA THR A 251 " pdb=" N THR A 251 " pdb=" C THR A 251 " pdb=" CB THR A 251 " both_signs ideal model delta sigma weight residual False 2.53 2.08 0.44 2.00e-01 2.50e+01 4.92e+00 chirality pdb=" CA ILE B 264 " pdb=" N ILE B 264 " pdb=" C ILE B 264 " pdb=" CB ILE B 264 " both_signs ideal model delta sigma weight residual False 2.43 2.79 -0.36 2.00e-01 2.50e+01 3.15e+00 chirality pdb=" CA LEU A 249 " pdb=" N LEU A 249 " pdb=" C LEU A 249 " pdb=" CB LEU A 249 " both_signs ideal model delta sigma weight residual False 2.51 2.23 0.28 2.00e-01 2.50e+01 1.92e+00 ... (remaining 664 not shown) Planarity restraints: 685 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 119 " 0.057 5.00e-02 4.00e+02 8.76e-02 1.23e+01 pdb=" N PRO A 120 " -0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 120 " 0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 120 " 0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASN A 115 " -0.041 5.00e-02 4.00e+02 6.27e-02 6.28e+00 pdb=" N PRO A 116 " 0.108 5.00e-02 4.00e+02 pdb=" CA PRO A 116 " -0.033 5.00e-02 4.00e+02 pdb=" CD PRO A 116 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 196 " -0.012 2.00e-02 2.50e+03 2.34e-02 5.45e+00 pdb=" C PHE A 196 " 0.040 2.00e-02 2.50e+03 pdb=" O PHE A 196 " -0.015 2.00e-02 2.50e+03 pdb=" N VAL A 197 " -0.013 2.00e-02 2.50e+03 ... (remaining 682 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.88: 1450 2.88 - 3.44: 5034 3.44 - 4.01: 7273 4.01 - 4.57: 10264 4.57 - 5.14: 14449 Nonbonded interactions: 38470 Sorted by model distance: nonbonded pdb=" OE2 GLU A 234 " pdb=" OH TYR A 266 " model vdw 2.309 3.040 nonbonded pdb=" O PRO A 116 " pdb=" NZ LYS B 84 " model vdw 2.335 3.120 nonbonded pdb=" NZ LYS A 84 " pdb=" O PRO B 116 " model vdw 2.349 3.120 nonbonded pdb=" C ILE A 264 " pdb=" OE1 GLU A 265 " model vdw 2.376 3.270 nonbonded pdb=" OE1 GLN A 231 " pdb=" OG SER A 241 " model vdw 2.414 3.040 ... (remaining 38465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 297) selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.670 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: 0.020 Process input model: 5.660 Find NCS groups from input model: 0.060 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:1.230 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 7.720 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 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 : 0.005 0.079 4218 Z= 0.268 Angle : 1.125 16.364 5723 Z= 0.634 Chirality : 0.059 0.444 667 Planarity : 0.008 0.088 685 Dihedral : 14.378 136.317 1475 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 0.23 % Allowed : 2.06 % Favored : 97.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.27 (0.35), residues: 513 helix: 2.42 (0.24), residues: 392 sheet: None (None), residues: 0 loop : -1.75 (0.51), residues: 121 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.016 0.002 TYR B 284 PHE 0.039 0.003 PHE A 276 TRP 0.031 0.002 TRP A 127 HIS 0.006 0.001 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00537 ( 4217) covalent geometry : angle 1.12476 ( 5721) SS BOND : bond 0.00323 ( 1) SS BOND : angle 0.51756 ( 2) hydrogen bonds : bond 0.10107 ( 323) hydrogen bonds : angle 4.66508 ( 969) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 227 time to evaluate : 0.091 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8274 (tttt) cc_final: 0.7236 (ttmm) REVERT: A 77 LYS cc_start: 0.9185 (mttm) cc_final: 0.8962 (mtpt) REVERT: A 82 GLN cc_start: 0.8363 (pt0) cc_final: 0.7628 (pp30) REVERT: A 86 ASP cc_start: 0.8291 (m-30) cc_final: 0.7641 (m-30) REVERT: A 104 LYS cc_start: 0.9424 (ttpp) cc_final: 0.9103 (ttpp) REVERT: A 105 GLN cc_start: 0.8742 (mt0) cc_final: 0.8438 (pt0) REVERT: A 195 MET cc_start: 0.8544 (tmm) cc_final: 0.7503 (tmm) REVERT: A 268 ASP cc_start: 0.7318 (t70) cc_final: 0.6973 (t0) REVERT: B 66 LYS cc_start: 0.8655 (ttpt) cc_final: 0.8204 (ttmm) REVERT: B 77 LYS cc_start: 0.9451 (mtmt) cc_final: 0.9248 (mtpt) REVERT: B 120 PRO cc_start: 0.8391 (Cg_endo) cc_final: 0.7370 (Cg_exo) outliers start: 1 outliers final: 0 residues processed: 227 average time/residue: 0.0669 time to fit residues: 18.8591 Evaluate side-chains 188 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 188 time to evaluate : 0.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 25 optimal weight: 3.9990 chunk 19 optimal weight: 0.0980 chunk 30 optimal weight: 0.0870 chunk 22 optimal weight: 0.7980 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 147 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 180 GLN B 91 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4135 r_free = 0.4135 target = 0.154954 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3594 r_free = 0.3594 target = 0.115474 restraints weight = 7318.809| |-----------------------------------------------------------------------------| r_work (start): 0.3537 rms_B_bonded: 4.15 r_work: 0.3361 rms_B_bonded: 4.96 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4218 Z= 0.167 Angle : 0.778 10.748 5723 Z= 0.403 Chirality : 0.045 0.178 667 Planarity : 0.005 0.040 685 Dihedral : 10.418 139.460 586 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 3.20 % Allowed : 15.33 % Favored : 81.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.70 (0.36), residues: 513 helix: 2.67 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.55 (0.54), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.001 ARG B 156 TYR 0.018 0.002 TYR B 57 PHE 0.021 0.002 PHE A 158 TRP 0.032 0.002 TRP A 199 HIS 0.006 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00369 ( 4217) covalent geometry : angle 0.77859 ( 5721) SS BOND : bond 0.00194 ( 1) SS BOND : angle 0.31441 ( 2) hydrogen bonds : bond 0.04370 ( 323) hydrogen bonds : angle 4.01823 ( 969) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 210 time to evaluate : 0.157 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8461 (tttt) cc_final: 0.7585 (ttmm) REVERT: A 70 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8126 (mm110) REVERT: A 73 GLU cc_start: 0.9060 (pt0) cc_final: 0.8709 (pt0) REVERT: A 79 ARG cc_start: 0.8777 (tmt-80) cc_final: 0.8204 (tpt90) REVERT: A 82 GLN cc_start: 0.8742 (pt0) cc_final: 0.8072 (pp30) REVERT: A 83 GLU cc_start: 0.8422 (tp30) cc_final: 0.8194 (tp30) REVERT: A 86 ASP cc_start: 0.8466 (m-30) cc_final: 0.8116 (m-30) REVERT: A 101 ASP cc_start: 0.8863 (t0) cc_final: 0.8559 (t0) REVERT: A 104 LYS cc_start: 0.9483 (ttpp) cc_final: 0.9151 (ttpp) REVERT: A 180 GLN cc_start: 0.8522 (OUTLIER) cc_final: 0.8307 (tp40) REVERT: A 221 LEU cc_start: 0.9420 (tt) cc_final: 0.9210 (pp) REVERT: A 263 GLU cc_start: 0.8642 (tt0) cc_final: 0.8250 (tt0) REVERT: A 268 ASP cc_start: 0.8178 (t70) cc_final: 0.7859 (t70) REVERT: A 269 TYR cc_start: 0.8010 (m-80) cc_final: 0.7787 (m-80) REVERT: A 284 TYR cc_start: 0.8972 (t80) cc_final: 0.8647 (t80) REVERT: B 44 TRP cc_start: 0.7583 (m-90) cc_final: 0.7278 (m-10) REVERT: B 45 LYS cc_start: 0.8469 (mtmm) cc_final: 0.7987 (mmtt) REVERT: B 48 LEU cc_start: 0.9262 (mt) cc_final: 0.9031 (mt) REVERT: B 50 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8391 (tt) REVERT: B 66 LYS cc_start: 0.9001 (ttpt) cc_final: 0.8352 (ttmt) REVERT: B 68 LEU cc_start: 0.9027 (mt) cc_final: 0.8818 (mp) REVERT: B 70 GLN cc_start: 0.9075 (mt0) cc_final: 0.8645 (mm-40) REVERT: B 73 GLU cc_start: 0.9086 (pt0) cc_final: 0.8430 (pt0) REVERT: B 115 ASN cc_start: 0.9242 (p0) cc_final: 0.9021 (p0) REVERT: B 122 GLN cc_start: 0.7377 (mp-120) cc_final: 0.6612 (mp10) REVERT: B 222 PHE cc_start: 0.7952 (m-80) cc_final: 0.7365 (m-10) REVERT: B 240 GLU cc_start: 0.8807 (mt-10) cc_final: 0.8532 (mt-10) REVERT: B 284 TYR cc_start: 0.9129 (t80) cc_final: 0.8929 (t80) outliers start: 14 outliers final: 5 residues processed: 214 average time/residue: 0.0683 time to fit residues: 18.0909 Evaluate side-chains 204 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 197 time to evaluate : 0.212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 VAL Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 0.3980 chunk 9 optimal weight: 0.8980 chunk 11 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 2 optimal weight: 0.7980 chunk 14 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 95 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4122 r_free = 0.4122 target = 0.153172 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3621 r_free = 0.3621 target = 0.117182 restraints weight = 7395.128| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 3.83 r_work: 0.3318 rms_B_bonded: 4.93 restraints_weight: 0.5000 r_work (final): 0.3318 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7882 moved from start: 0.3638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4218 Z= 0.166 Angle : 0.775 10.301 5723 Z= 0.392 Chirality : 0.044 0.190 667 Planarity : 0.004 0.048 685 Dihedral : 10.338 136.023 586 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.81 % Allowed : 18.76 % Favored : 76.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.65 (0.36), residues: 513 helix: 2.58 (0.24), residues: 397 sheet: None (None), residues: 0 loop : -1.36 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG A 207 TYR 0.022 0.002 TYR A 162 PHE 0.019 0.002 PHE A 158 TRP 0.021 0.001 TRP A 295 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00382 ( 4217) covalent geometry : angle 0.77539 ( 5721) SS BOND : bond 0.00087 ( 1) SS BOND : angle 0.33017 ( 2) hydrogen bonds : bond 0.04162 ( 323) hydrogen bonds : angle 3.93691 ( 969) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 204 time to evaluate : 0.146 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8524 (tttt) cc_final: 0.7639 (ttmm) REVERT: A 70 GLN cc_start: 0.8511 (mm-40) cc_final: 0.8268 (mm110) REVERT: A 82 GLN cc_start: 0.8726 (pt0) cc_final: 0.7916 (pp30) REVERT: A 86 ASP cc_start: 0.8543 (m-30) cc_final: 0.7981 (m-30) REVERT: A 101 ASP cc_start: 0.8899 (t0) cc_final: 0.8638 (t0) REVERT: A 104 LYS cc_start: 0.9486 (ttpp) cc_final: 0.9204 (ttpp) REVERT: A 162 TYR cc_start: 0.9022 (t80) cc_final: 0.8782 (t80) REVERT: A 187 LYS cc_start: 0.8093 (OUTLIER) cc_final: 0.7626 (pttt) REVERT: A 284 TYR cc_start: 0.9003 (t80) cc_final: 0.8710 (t80) REVERT: B 44 TRP cc_start: 0.7614 (m-90) cc_final: 0.7296 (m-10) REVERT: B 48 LEU cc_start: 0.9059 (mt) cc_final: 0.8784 (mt) REVERT: B 50 ILE cc_start: 0.8672 (OUTLIER) cc_final: 0.8405 (tt) REVERT: B 66 LYS cc_start: 0.8995 (ttpt) cc_final: 0.8352 (ttmm) REVERT: B 68 LEU cc_start: 0.9055 (mt) cc_final: 0.8830 (mp) REVERT: B 70 GLN cc_start: 0.9082 (mt0) cc_final: 0.8670 (mm-40) REVERT: B 158 PHE cc_start: 0.9256 (t80) cc_final: 0.9010 (t80) REVERT: B 222 PHE cc_start: 0.8090 (m-80) cc_final: 0.7884 (m-10) REVERT: B 240 GLU cc_start: 0.8842 (mt-10) cc_final: 0.8522 (mt-10) REVERT: B 295 TRP cc_start: 0.7885 (OUTLIER) cc_final: 0.7250 (m100) outliers start: 21 outliers final: 9 residues processed: 208 average time/residue: 0.0746 time to fit residues: 18.9889 Evaluate side-chains 214 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 202 time to evaluate : 0.119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 167 ILE Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Chi-restraints excluded: chain B residue 295 TRP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 43 optimal weight: 3.9990 chunk 8 optimal weight: 0.0000 chunk 44 optimal weight: 0.7980 chunk 27 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 chunk 26 optimal weight: 0.6980 chunk 46 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 3 optimal weight: 0.7980 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.4132 r_free = 0.4132 target = 0.153243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3627 r_free = 0.3627 target = 0.116653 restraints weight = 7294.844| |-----------------------------------------------------------------------------| r_work (start): 0.3515 rms_B_bonded: 4.01 r_work (final): 0.3515 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7852 moved from start: 0.3976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 4218 Z= 0.165 Angle : 0.795 10.731 5723 Z= 0.398 Chirality : 0.045 0.189 667 Planarity : 0.004 0.040 685 Dihedral : 10.142 132.612 586 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 11.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 4.12 % Allowed : 22.88 % Favored : 73.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.47 (0.36), residues: 513 helix: 2.45 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.42 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 207 TYR 0.020 0.002 TYR A 162 PHE 0.022 0.002 PHE A 158 TRP 0.016 0.001 TRP A 295 HIS 0.001 0.000 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00379 ( 4217) covalent geometry : angle 0.79550 ( 5721) SS BOND : bond 0.00025 ( 1) SS BOND : angle 0.31141 ( 2) hydrogen bonds : bond 0.04204 ( 323) hydrogen bonds : angle 3.83620 ( 969) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 212 time to evaluate : 0.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 TYR cc_start: 0.8277 (t80) cc_final: 0.8068 (t80) REVERT: A 66 LYS cc_start: 0.8541 (tttt) cc_final: 0.7712 (ttmm) REVERT: A 70 GLN cc_start: 0.8445 (mm110) cc_final: 0.8027 (mm110) REVERT: A 82 GLN cc_start: 0.8636 (pt0) cc_final: 0.7705 (pp30) REVERT: A 83 GLU cc_start: 0.8525 (tp30) cc_final: 0.8147 (tp30) REVERT: A 86 ASP cc_start: 0.8510 (m-30) cc_final: 0.7889 (m-30) REVERT: A 104 LYS cc_start: 0.9483 (ttpp) cc_final: 0.9234 (ttpp) REVERT: A 187 LYS cc_start: 0.8046 (OUTLIER) cc_final: 0.7637 (pttt) REVERT: A 268 ASP cc_start: 0.8247 (OUTLIER) cc_final: 0.7495 (t70) REVERT: B 43 LYS cc_start: 0.8044 (tptt) cc_final: 0.7493 (tptt) REVERT: B 45 LYS cc_start: 0.8645 (mtmm) cc_final: 0.8351 (pttp) REVERT: B 66 LYS cc_start: 0.9035 (ttpt) cc_final: 0.8633 (ptmm) REVERT: B 68 LEU cc_start: 0.8916 (mt) cc_final: 0.8715 (mp) REVERT: B 70 GLN cc_start: 0.8846 (mt0) cc_final: 0.8643 (mm-40) REVERT: B 72 GLU cc_start: 0.9071 (tp30) cc_final: 0.8828 (tp30) REVERT: B 86 ASP cc_start: 0.8919 (p0) cc_final: 0.8628 (p0) REVERT: B 100 GLU cc_start: 0.9020 (mm-30) cc_final: 0.8804 (mm-30) REVERT: B 104 LYS cc_start: 0.9379 (ttmm) cc_final: 0.9023 (mtmm) REVERT: B 158 PHE cc_start: 0.9219 (t80) cc_final: 0.9010 (t80) REVERT: B 180 GLN cc_start: 0.8922 (tt0) cc_final: 0.8656 (tt0) REVERT: B 240 GLU cc_start: 0.8639 (mt-10) cc_final: 0.8268 (mt-10) REVERT: B 265 GLU cc_start: 0.8623 (pm20) cc_final: 0.8340 (pm20) REVERT: B 291 MET cc_start: 0.8598 (tmm) cc_final: 0.7933 (mmp) outliers start: 18 outliers final: 8 residues processed: 218 average time/residue: 0.0664 time to fit residues: 17.9875 Evaluate side-chains 198 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 188 time to evaluate : 0.159 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 96 THR Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 31 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 8 optimal weight: 0.0170 chunk 2 optimal weight: 2.9990 chunk 45 optimal weight: 0.5980 chunk 6 optimal weight: 0.7980 chunk 25 optimal weight: 0.2980 chunk 15 optimal weight: 0.0470 chunk 0 optimal weight: 6.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 91 HIS A 180 GLN ** B 105 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4177 r_free = 0.4177 target = 0.155125 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3726 r_free = 0.3726 target = 0.121592 restraints weight = 7368.446| |-----------------------------------------------------------------------------| r_work (start): 0.3645 rms_B_bonded: 3.65 r_work: 0.3466 rms_B_bonded: 4.55 restraints_weight: 0.5000 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.4409 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4218 Z= 0.157 Angle : 0.818 11.639 5723 Z= 0.409 Chirality : 0.044 0.187 667 Planarity : 0.004 0.044 685 Dihedral : 9.895 129.807 586 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 12.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.97 % Allowed : 28.15 % Favored : 68.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.36), residues: 513 helix: 2.39 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.42 (0.56), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 79 TYR 0.019 0.002 TYR B 57 PHE 0.018 0.001 PHE A 158 TRP 0.016 0.001 TRP A 295 HIS 0.007 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00349 ( 4217) covalent geometry : angle 0.81833 ( 5721) SS BOND : bond 0.00016 ( 1) SS BOND : angle 0.20987 ( 2) hydrogen bonds : bond 0.04190 ( 323) hydrogen bonds : angle 3.89922 ( 969) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 206 time to evaluate : 0.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8682 (tppt) cc_final: 0.8459 (tppt) REVERT: A 66 LYS cc_start: 0.8659 (tttt) cc_final: 0.7884 (ttmm) REVERT: A 70 GLN cc_start: 0.8619 (mm110) cc_final: 0.8130 (mm110) REVERT: A 82 GLN cc_start: 0.8668 (pt0) cc_final: 0.7830 (pp30) REVERT: A 83 GLU cc_start: 0.8496 (tp30) cc_final: 0.8179 (tp30) REVERT: A 86 ASP cc_start: 0.8531 (m-30) cc_final: 0.8104 (m-30) REVERT: A 104 LYS cc_start: 0.9487 (ttpp) cc_final: 0.9230 (ttpp) REVERT: A 187 LYS cc_start: 0.8273 (OUTLIER) cc_final: 0.7709 (pttt) REVERT: A 263 GLU cc_start: 0.8605 (tt0) cc_final: 0.8275 (tm-30) REVERT: A 268 ASP cc_start: 0.8145 (OUTLIER) cc_final: 0.7524 (t70) REVERT: A 269 TYR cc_start: 0.8123 (m-80) cc_final: 0.7828 (m-80) REVERT: B 43 LYS cc_start: 0.8124 (tptt) cc_final: 0.7841 (tptt) REVERT: B 45 LYS cc_start: 0.8684 (mtmm) cc_final: 0.8257 (pttt) REVERT: B 48 LEU cc_start: 0.9010 (mt) cc_final: 0.8770 (mt) REVERT: B 66 LYS cc_start: 0.8981 (ttpt) cc_final: 0.8310 (ttmt) REVERT: B 68 LEU cc_start: 0.8955 (mt) cc_final: 0.8708 (mp) REVERT: B 70 GLN cc_start: 0.9037 (mt0) cc_final: 0.8673 (mm-40) REVERT: B 86 ASP cc_start: 0.8814 (p0) cc_final: 0.8419 (p0) REVERT: B 104 LYS cc_start: 0.9399 (ttmm) cc_final: 0.9170 (mtmm) REVERT: B 195 MET cc_start: 0.7441 (mmm) cc_final: 0.7052 (mpp) REVERT: B 222 PHE cc_start: 0.7982 (m-80) cc_final: 0.7774 (m-10) REVERT: B 240 GLU cc_start: 0.8854 (mt-10) cc_final: 0.8563 (mt-10) REVERT: B 291 MET cc_start: 0.8460 (tmm) cc_final: 0.7870 (mmp) outliers start: 13 outliers final: 7 residues processed: 208 average time/residue: 0.0705 time to fit residues: 18.0423 Evaluate side-chains 206 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 197 time to evaluate : 0.139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 68 LEU Chi-restraints excluded: chain A residue 180 GLN Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 101 ASP Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 28 optimal weight: 3.9990 chunk 8 optimal weight: 0.8980 chunk 44 optimal weight: 0.3980 chunk 47 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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 = 0.4149 r_free = 0.4149 target = 0.152750 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3672 r_free = 0.3672 target = 0.118405 restraints weight = 7460.597| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 3.72 r_work: 0.3388 rms_B_bonded: 4.75 restraints_weight: 0.5000 r_work (final): 0.3388 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.4607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 4218 Z= 0.174 Angle : 0.855 12.829 5723 Z= 0.424 Chirality : 0.046 0.267 667 Planarity : 0.004 0.035 685 Dihedral : 9.906 127.617 586 Min Nonbonded Distance : 2.491 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 3.66 % Allowed : 28.38 % Favored : 67.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.39 (0.37), residues: 513 helix: 2.38 (0.25), residues: 398 sheet: None (None), residues: 0 loop : -1.41 (0.57), residues: 115 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 207 TYR 0.022 0.002 TYR A 162 PHE 0.018 0.001 PHE A 158 TRP 0.012 0.001 TRP A 295 HIS 0.002 0.000 HIS A 91 Details of bonding type rmsd covalent geometry : bond 0.00408 ( 4217) covalent geometry : angle 0.85530 ( 5721) SS BOND : bond 0.00032 ( 1) SS BOND : angle 0.14175 ( 2) hydrogen bonds : bond 0.04238 ( 323) hydrogen bonds : angle 3.86219 ( 969) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 203 time to evaluate : 0.127 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8738 (tppt) cc_final: 0.8491 (tppt) REVERT: A 66 LYS cc_start: 0.8760 (tttt) cc_final: 0.7939 (ttmm) REVERT: A 70 GLN cc_start: 0.8643 (mm110) cc_final: 0.8280 (mm110) REVERT: A 79 ARG cc_start: 0.8149 (ptp-110) cc_final: 0.7860 (ptp-170) REVERT: A 82 GLN cc_start: 0.8723 (pt0) cc_final: 0.7821 (pp30) REVERT: A 83 GLU cc_start: 0.8503 (tp30) cc_final: 0.8138 (tp30) REVERT: A 86 ASP cc_start: 0.8494 (m-30) cc_final: 0.8050 (m-30) REVERT: A 187 LYS cc_start: 0.8353 (OUTLIER) cc_final: 0.7793 (pttt) REVERT: A 207 ARG cc_start: 0.8960 (mtm180) cc_final: 0.8667 (mtm180) REVERT: A 263 GLU cc_start: 0.8670 (tt0) cc_final: 0.8335 (tm-30) REVERT: A 268 ASP cc_start: 0.8221 (OUTLIER) cc_final: 0.7606 (t70) REVERT: A 269 TYR cc_start: 0.8213 (m-80) cc_final: 0.7934 (m-80) REVERT: B 43 LYS cc_start: 0.8212 (tptt) cc_final: 0.7804 (tptt) REVERT: B 51 PHE cc_start: 0.9297 (t80) cc_final: 0.9064 (t80) REVERT: B 66 LYS cc_start: 0.9017 (ttpt) cc_final: 0.8351 (ttmt) REVERT: B 68 LEU cc_start: 0.8916 (mt) cc_final: 0.8678 (mp) REVERT: B 70 GLN cc_start: 0.9060 (mt0) cc_final: 0.8736 (mm-40) REVERT: B 73 GLU cc_start: 0.9014 (pt0) cc_final: 0.8595 (pt0) REVERT: B 86 ASP cc_start: 0.8807 (p0) cc_final: 0.8396 (p0) REVERT: B 104 LYS cc_start: 0.9377 (ttmm) cc_final: 0.9143 (mtmm) REVERT: B 195 MET cc_start: 0.7432 (mmm) cc_final: 0.7138 (mpp) REVERT: B 222 PHE cc_start: 0.8052 (m-80) cc_final: 0.7791 (m-10) REVERT: B 240 GLU cc_start: 0.8857 (mt-10) cc_final: 0.8579 (mt-10) outliers start: 16 outliers final: 11 residues processed: 207 average time/residue: 0.0721 time to fit residues: 18.3959 Evaluate side-chains 206 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 193 time to evaluate : 0.121 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 181 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 0.9980 chunk 4 optimal weight: 0.6980 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 0.3980 chunk 49 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 43 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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 = 0.4008 r_free = 0.4008 target = 0.145427 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3511 r_free = 0.3511 target = 0.111389 restraints weight = 7823.369| |-----------------------------------------------------------------------------| r_work (start): 0.3438 rms_B_bonded: 4.14 r_work (final): 0.3438 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7666 moved from start: 0.4784 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4218 Z= 0.170 Angle : 0.869 12.138 5723 Z= 0.426 Chirality : 0.046 0.236 667 Planarity : 0.004 0.034 685 Dihedral : 9.865 125.282 586 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.90 % Favored : 96.10 % Rotamer: Outliers : 3.20 % Allowed : 29.29 % Favored : 67.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.26 (0.36), residues: 513 helix: 2.31 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.51 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.021 0.002 TYR A 162 PHE 0.013 0.001 PHE B 196 TRP 0.012 0.001 TRP A 295 HIS 0.002 0.001 HIS B 232 Details of bonding type rmsd covalent geometry : bond 0.00397 ( 4217) covalent geometry : angle 0.86925 ( 5721) SS BOND : bond 0.00019 ( 1) SS BOND : angle 0.22646 ( 2) hydrogen bonds : bond 0.04307 ( 323) hydrogen bonds : angle 3.89133 ( 969) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 193 time to evaluate : 0.156 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8726 (tppt) cc_final: 0.8476 (tppt) REVERT: A 66 LYS cc_start: 0.8503 (tttt) cc_final: 0.7592 (ttmm) REVERT: A 70 GLN cc_start: 0.8294 (mm110) cc_final: 0.7876 (mm110) REVERT: A 79 ARG cc_start: 0.8236 (ptp-110) cc_final: 0.7872 (ptp90) REVERT: A 82 GLN cc_start: 0.8635 (pt0) cc_final: 0.7783 (pp30) REVERT: A 83 GLU cc_start: 0.8719 (tp30) cc_final: 0.8209 (tp30) REVERT: A 86 ASP cc_start: 0.8608 (m-30) cc_final: 0.8110 (m-30) REVERT: A 187 LYS cc_start: 0.8262 (OUTLIER) cc_final: 0.7909 (pttt) REVERT: A 263 GLU cc_start: 0.8737 (tt0) cc_final: 0.8287 (tm-30) REVERT: A 268 ASP cc_start: 0.8359 (OUTLIER) cc_final: 0.7659 (p0) REVERT: B 45 LYS cc_start: 0.8688 (mttt) cc_final: 0.8368 (mmtt) REVERT: B 66 LYS cc_start: 0.8904 (ttpt) cc_final: 0.8627 (ttpp) REVERT: B 70 GLN cc_start: 0.8919 (mt0) cc_final: 0.8398 (mm-40) REVERT: B 104 LYS cc_start: 0.9308 (ttmm) cc_final: 0.9066 (mtmm) REVERT: B 105 GLN cc_start: 0.8372 (mp10) cc_final: 0.8139 (mp10) REVERT: B 222 PHE cc_start: 0.8014 (m-80) cc_final: 0.7686 (m-10) REVERT: B 240 GLU cc_start: 0.8694 (mt-10) cc_final: 0.8315 (mt-10) REVERT: B 291 MET cc_start: 0.8662 (tmm) cc_final: 0.7612 (mmp) outliers start: 14 outliers final: 9 residues processed: 198 average time/residue: 0.0723 time to fit residues: 17.4423 Evaluate side-chains 202 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 268 ASP Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 128 ASP Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 249 LEU Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 7 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.4980 chunk 26 optimal weight: 1.9990 chunk 2 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 40 optimal weight: 0.1980 chunk 18 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 49 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.145278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3499 r_free = 0.3499 target = 0.110969 restraints weight = 7774.214| |-----------------------------------------------------------------------------| r_work (start): 0.3439 rms_B_bonded: 4.18 r_work (final): 0.3439 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7648 moved from start: 0.4985 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4218 Z= 0.170 Angle : 0.899 12.350 5723 Z= 0.443 Chirality : 0.047 0.190 667 Planarity : 0.004 0.035 685 Dihedral : 9.788 121.925 586 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 13.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.52 % Allowed : 30.66 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.15 (0.37), residues: 513 helix: 2.24 (0.25), residues: 397 sheet: None (None), residues: 0 loop : -1.59 (0.57), residues: 116 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 156 TYR 0.015 0.002 TYR A 162 PHE 0.013 0.001 PHE B 51 TRP 0.016 0.001 TRP A 295 HIS 0.001 0.000 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00393 ( 4217) covalent geometry : angle 0.89932 ( 5721) SS BOND : bond 0.00023 ( 1) SS BOND : angle 0.17169 ( 2) hydrogen bonds : bond 0.04348 ( 323) hydrogen bonds : angle 3.85219 ( 969) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 198 time to evaluate : 0.152 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8697 (tppt) cc_final: 0.8461 (tppt) REVERT: A 66 LYS cc_start: 0.8481 (tttt) cc_final: 0.7581 (ttmm) REVERT: A 70 GLN cc_start: 0.8291 (mm110) cc_final: 0.7849 (mm110) REVERT: A 82 GLN cc_start: 0.8680 (pt0) cc_final: 0.7789 (pp30) REVERT: A 83 GLU cc_start: 0.8724 (tp30) cc_final: 0.8175 (tp30) REVERT: A 86 ASP cc_start: 0.8601 (m-30) cc_final: 0.8093 (m-30) REVERT: A 187 LYS cc_start: 0.8103 (OUTLIER) cc_final: 0.7762 (pttt) REVERT: A 263 GLU cc_start: 0.8737 (tt0) cc_final: 0.8340 (tm-30) REVERT: B 43 LYS cc_start: 0.8014 (tptt) cc_final: 0.7543 (tptt) REVERT: B 45 LYS cc_start: 0.8643 (mttt) cc_final: 0.8277 (pttp) REVERT: B 66 LYS cc_start: 0.8895 (ttpt) cc_final: 0.8139 (ttmt) REVERT: B 70 GLN cc_start: 0.8908 (mt0) cc_final: 0.8459 (mm-40) REVERT: B 104 LYS cc_start: 0.9266 (ttmm) cc_final: 0.9015 (mtmm) REVERT: B 105 GLN cc_start: 0.8464 (mp10) cc_final: 0.8231 (mp10) REVERT: B 180 GLN cc_start: 0.8876 (tt0) cc_final: 0.8292 (tp40) REVERT: B 222 PHE cc_start: 0.8013 (m-10) cc_final: 0.7685 (m-10) REVERT: B 240 GLU cc_start: 0.8667 (mt-10) cc_final: 0.8291 (mt-10) REVERT: B 291 MET cc_start: 0.8640 (tmm) cc_final: 0.7633 (mmp) outliers start: 11 outliers final: 7 residues processed: 202 average time/residue: 0.0691 time to fit residues: 17.1515 Evaluate side-chains 197 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 189 time to evaluate : 0.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 18 optimal weight: 0.5980 chunk 46 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 15 optimal weight: 0.0370 chunk 29 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 7 optimal weight: 0.0070 chunk 23 optimal weight: 0.9990 chunk 11 optimal weight: 0.4980 chunk 17 optimal weight: 0.9990 overall best weight: 0.4276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4001 r_free = 0.4001 target = 0.145051 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3461 r_free = 0.3461 target = 0.109158 restraints weight = 7891.663| |-----------------------------------------------------------------------------| r_work (start): 0.3428 rms_B_bonded: 4.53 r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.5080 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4218 Z= 0.170 Angle : 0.928 12.668 5723 Z= 0.452 Chirality : 0.047 0.194 667 Planarity : 0.004 0.041 685 Dihedral : 9.651 117.705 586 Min Nonbonded Distance : 2.344 Molprobity Statistics. All-atom Clashscore : 13.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer: Outliers : 2.97 % Allowed : 30.66 % Favored : 66.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.08 (0.37), residues: 513 helix: 2.20 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -1.64 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 207 TYR 0.022 0.002 TYR B 57 PHE 0.029 0.001 PHE B 158 TRP 0.013 0.001 TRP A 295 HIS 0.001 0.000 HIS B 91 Details of bonding type rmsd covalent geometry : bond 0.00391 ( 4217) covalent geometry : angle 0.92842 ( 5721) SS BOND : bond 0.00046 ( 1) SS BOND : angle 0.22623 ( 2) hydrogen bonds : bond 0.04315 ( 323) hydrogen bonds : angle 3.85744 ( 969) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 197 time to evaluate : 0.116 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 43 LYS cc_start: 0.8731 (tppt) cc_final: 0.8299 (tppt) REVERT: A 66 LYS cc_start: 0.8446 (tttt) cc_final: 0.7624 (ttmm) REVERT: A 70 GLN cc_start: 0.8359 (mm110) cc_final: 0.7881 (mm110) REVERT: A 82 GLN cc_start: 0.8637 (pt0) cc_final: 0.7790 (pp30) REVERT: A 83 GLU cc_start: 0.8779 (tp30) cc_final: 0.8234 (tp30) REVERT: A 86 ASP cc_start: 0.8632 (m-30) cc_final: 0.8127 (m-30) REVERT: A 158 PHE cc_start: 0.9226 (t80) cc_final: 0.9022 (t80) REVERT: A 187 LYS cc_start: 0.8091 (OUTLIER) cc_final: 0.7753 (pttt) REVERT: A 263 GLU cc_start: 0.8789 (tt0) cc_final: 0.8391 (tm-30) REVERT: B 43 LYS cc_start: 0.7915 (tptt) cc_final: 0.7558 (tptt) REVERT: B 45 LYS cc_start: 0.8668 (mttt) cc_final: 0.8260 (pttp) REVERT: B 66 LYS cc_start: 0.8866 (ttpt) cc_final: 0.8124 (ttmt) REVERT: B 70 GLN cc_start: 0.8902 (mt0) cc_final: 0.8431 (mm-40) REVERT: B 104 LYS cc_start: 0.9264 (ttmm) cc_final: 0.9024 (mtmm) REVERT: B 105 GLN cc_start: 0.8491 (mp10) cc_final: 0.8205 (mp10) REVERT: B 122 GLN cc_start: 0.8452 (tp40) cc_final: 0.8246 (mm-40) REVERT: B 222 PHE cc_start: 0.8100 (m-10) cc_final: 0.7745 (m-10) REVERT: B 240 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8288 (mt-10) REVERT: B 291 MET cc_start: 0.8636 (tmm) cc_final: 0.7851 (mmp) outliers start: 13 outliers final: 10 residues processed: 200 average time/residue: 0.0731 time to fit residues: 17.7241 Evaluate side-chains 202 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 30 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 5 optimal weight: 2.9990 chunk 40 optimal weight: 0.0470 chunk 17 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 3 optimal weight: 0.0970 overall best weight: 0.5678 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.143392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3445 r_free = 0.3445 target = 0.108214 restraints weight = 7720.417| |-----------------------------------------------------------------------------| r_work (start): 0.3432 rms_B_bonded: 4.41 r_work (final): 0.3432 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7637 moved from start: 0.5280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 4218 Z= 0.177 Angle : 0.954 12.573 5723 Z= 0.468 Chirality : 0.046 0.174 667 Planarity : 0.004 0.036 685 Dihedral : 9.602 115.344 586 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 14.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.09 % Favored : 95.91 % Rotamer: Outliers : 2.52 % Allowed : 31.81 % Favored : 65.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 2.04 (0.37), residues: 513 helix: 2.17 (0.25), residues: 396 sheet: None (None), residues: 0 loop : -1.66 (0.56), residues: 117 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 207 TYR 0.023 0.002 TYR B 57 PHE 0.026 0.001 PHE B 158 TRP 0.029 0.002 TRP A 199 HIS 0.002 0.001 HIS A 232 Details of bonding type rmsd covalent geometry : bond 0.00417 ( 4217) covalent geometry : angle 0.95454 ( 5721) SS BOND : bond 0.00012 ( 1) SS BOND : angle 0.17247 ( 2) hydrogen bonds : bond 0.04376 ( 323) hydrogen bonds : angle 3.89868 ( 969) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1026 Ramachandran restraints generated. 513 Oldfield, 0 Emsley, 513 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 191 time to evaluate : 0.167 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 LYS cc_start: 0.8459 (tttt) cc_final: 0.7627 (ttmm) REVERT: A 70 GLN cc_start: 0.8368 (mm110) cc_final: 0.7890 (mm110) REVERT: A 82 GLN cc_start: 0.8688 (pt0) cc_final: 0.7824 (pp30) REVERT: A 83 GLU cc_start: 0.8831 (tp30) cc_final: 0.8367 (tp30) REVERT: A 86 ASP cc_start: 0.8643 (m-30) cc_final: 0.8147 (m-30) REVERT: A 187 LYS cc_start: 0.8111 (OUTLIER) cc_final: 0.7782 (pttt) REVERT: A 207 ARG cc_start: 0.8983 (mtm180) cc_final: 0.8599 (mtm180) REVERT: A 263 GLU cc_start: 0.8866 (tt0) cc_final: 0.8473 (tm-30) REVERT: B 43 LYS cc_start: 0.7938 (tptt) cc_final: 0.7564 (tptt) REVERT: B 45 LYS cc_start: 0.8671 (mttt) cc_final: 0.8268 (pttp) REVERT: B 66 LYS cc_start: 0.8884 (ttpt) cc_final: 0.8134 (ttmt) REVERT: B 70 GLN cc_start: 0.8920 (mt0) cc_final: 0.8456 (mm-40) REVERT: B 104 LYS cc_start: 0.9255 (ttmm) cc_final: 0.9025 (mtmm) REVERT: B 105 GLN cc_start: 0.8458 (mp10) cc_final: 0.8164 (mp10) REVERT: B 122 GLN cc_start: 0.8460 (tp40) cc_final: 0.8228 (mm-40) REVERT: B 222 PHE cc_start: 0.8102 (m-10) cc_final: 0.7753 (m-10) REVERT: B 240 GLU cc_start: 0.8662 (mt-10) cc_final: 0.8304 (mt-10) REVERT: B 291 MET cc_start: 0.8556 (tmm) cc_final: 0.7844 (mmp) outliers start: 11 outliers final: 10 residues processed: 194 average time/residue: 0.0748 time to fit residues: 17.7210 Evaluate side-chains 200 residues out of total 437 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 189 time to evaluate : 0.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LEU Chi-restraints excluded: chain A residue 149 SER Chi-restraints excluded: chain A residue 169 LEU Chi-restraints excluded: chain A residue 187 LYS Chi-restraints excluded: chain A residue 248 THR Chi-restraints excluded: chain A residue 289 LEU Chi-restraints excluded: chain B residue 88 LEU Chi-restraints excluded: chain B residue 115 ASN Chi-restraints excluded: chain B residue 148 VAL Chi-restraints excluded: chain B residue 219 CYS Chi-restraints excluded: chain B residue 282 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 48 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 42 optimal weight: 0.9990 chunk 41 optimal weight: 3.9990 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 0.9990 chunk 33 optimal weight: 0.9980 chunk 44 optimal weight: 0.0040 chunk 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.3980 chunk 10 optimal weight: 0.9980 overall best weight: 0.5992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 115 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.145956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.111182 restraints weight = 7712.073| |-----------------------------------------------------------------------------| r_work (start): 0.3441 rms_B_bonded: 4.20 r_work (final): 0.3441 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.5326 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4218 Z= 0.182 Angle : 0.973 12.514 5723 Z= 0.480 Chirality : 0.048 0.178 667 Planarity : 0.004 0.037 685 Dihedral : 9.619 113.510 586 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 14.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 2.52 % Allowed : 32.49 % Favored : 64.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.98 (0.37), residues: 513 helix: 2.17 (0.25), residues: 394 sheet: None (None), residues: 0 loop : -1.77 (0.56), residues: 119 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 207 TYR 0.023 0.002 TYR B 57 PHE 0.026 0.001 PHE A 158 TRP 0.022 0.002 TRP A 199 HIS 0.002 0.001 HIS B 151 Details of bonding type rmsd covalent geometry : bond 0.00426 ( 4217) covalent geometry : angle 0.97330 ( 5721) SS BOND : bond 0.00031 ( 1) SS BOND : angle 0.13633 ( 2) hydrogen bonds : bond 0.04395 ( 323) hydrogen bonds : angle 3.92270 ( 969) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1136.92 seconds wall clock time: 20 minutes 5.61 seconds (1205.61 seconds total)